| Previous changeset 9:67906d99d3c0 (2018-01-22) Next changeset 11:0f445c315a08 (2018-08-23) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4 |
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modified:
abundance_estimates_to_matrix.xml macros.xml test-data/count/analyze_diff_expr/results.matrix test-data/count/analyze_diff_expr/results.matrix.RData test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat test-data/count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf test-data/count/analyze_diff_expr/results.matrix.log2.dat test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf test-data/count/contig_exn50_statistic/ExN50.stats test-data/count/define_clusters_by_cutting_tree/my_cluster_plots.pdf test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.MA_n_Volcano.pdf test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf test-data/count/qcheck/input.matrix.CPM.log2.sample_cor_matrix.pdf test-data/count/qcheck/wt_37.rep_compare.pdf test-data/count/qcheck/wt_ph8.rep_compare.pdf test-data/raw/Trinity.fasta |
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added:
test-data/count/Trinity.map test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.DE.subset.GOseq.enriched test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset test-data/count/qcheck/input.matrix.CPM.log2.prcomp.principal_components.pdf test-data/norm/Trinity.map test-data/norm/Trinity_paired_unmerged_1.fasta test-data/norm/Trinity_paired_unmerged_1.map test-data/raw/Trinity.map test-data/raw/Trinity_single_unmerged_1.fasta test-data/raw/Trinity_single_unmerged_1.map test-data/supertranscripts/trinity_genes.fasta test-data/supertranscripts/trinity_genes.gtf test-data/supertranscripts/trinity_genes.malign |
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removed:
test-data/count/qcheck/input.matrix.CPM.log2.principal_components.pdf |
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| diff -r 67906d99d3c0 -r 13ab393ba794 abundance_estimates_to_matrix.xml --- a/abundance_estimates_to_matrix.xml Mon Jan 22 11:28:19 2018 -0500 +++ b/abundance_estimates_to_matrix.xml Thu Jun 14 03:12:12 2018 -0400 |
| [ |
| @@ -1,12 +1,12 @@ -<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@.2"> +<tool id="trinity_abundance_estimates_to_matrix" name="Build expression matrix" version="@WRAPPER_VERSION@"> <description>for a de novo assembly of RNA-Seq data by Trinity</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"> - <requirement type="package" version="3.20.1">bioconductor-edger</requirement> + <requirement type="package" version="3.20.7">bioconductor-edger</requirement> <requirement type="package" version="0.9.1">salmon</requirement> - <requirement type="package" version="0.43.1">kallisto</requirement> + <requirement type="package" version="0.44.0">kallisto</requirement> </expand> <command detect_errors="aggressive"><![CDATA[ #import re @@ -19,13 +19,38 @@ --est_method ${est_method} --cross_sample_norm ${additional_params.cross_sample_norm} + #if $gene_trans_map: + --gene_trans_map '$gene_trans_map' + #else: + --gene_trans_map 'none' + #end if + #for $entry in $samples: '${re.sub('[^\w\-_]', '_', entry.element_identifier)}' #end for + + && mv *.isoform.counts.matrix '$trans_counts' + && mv *.isoform.TPM.not_cross_norm '$TPM_no_norm' + #if $gene_trans_map: + && mv *.gene.counts.matrix '$trans_counts_gene' + && mv *.gene.TPM.not_cross_norm '$TPM_no_norm_gene' + #end if + + #if $additional_params.cross_sample_norm == "TMM": + && mv *.isoform.TMM.EXPR.matrix '$norm_TMM' + #if $gene_trans_map: + && mv *.gene.TMM.EXPR.matrix '$norm_TMM_gene' + #end if + #else if $additional_params.cross_sample_norm == "UpperQuartile": + && mv *.isoform.UpperQuartile.EXPR.matrix '$norm_UQ' + #if $gene_trans_map: + && mv *.gene.UpperQuartile.EXPR.matrix '$norm_UQ_gene' + #end if + #end if ]]></command> <inputs> <param name="samples" label="Abundance estimates" type="data" multiple="true" format="tabular" help="output(s) from 'Align reads and estimate abundance' tool" /> - + <param format="tabular" name="gene_trans_map" argument="--gene_trans_map" type="data" label="Gene to transcript correspondence ('gene(tab)transcript' lines)" optional="true" help="Only needed for gene level estimates" /> <param type="select" name="est_method" argument="--est_method" label="Abundance estimation method"> <option value="RSEM">RSEM</option> <option value="eXpress">eXpress</option> @@ -42,14 +67,29 @@ </section> </inputs> <outputs> - <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment counts (raw counts)" from_work_dir="matrix.counts.matrix"/> - <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of TPM expression values (not cross-sample normalized)" from_work_dir="matrix.TPM.not_cross_norm"/> - <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values" from_work_dir="matrix.TMM.EXPR.matrix"> + <data format="tabular" name="trans_counts" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment isoform counts (raw counts)"/> + <data format="tabular" name="TPM_no_norm" label="${tool.name} on ${on_string}: matrix of isoform TPM expression values (not cross-sample normalized)"/> + + <data format="tabular" name="trans_counts_gene" label="${tool.name} on ${on_string}: estimated RNA-Seq fragment gene counts (raw counts)"> + <filter>gene_trans_map</filter> + </data> + <data format="tabular" name="TPM_no_norm_gene" label="${tool.name} on ${on_string}: matrix of gene TPM expression values (not cross-sample normalized)"> + <filter>gene_trans_map</filter> + </data> + + <data format="tabular" name="norm_TMM" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values"> <filter>additional_params['cross_sample_norm'] == "TMM"</filter> </data> - <data format="tabular" name="norm" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values" from_work_dir="matrix.UpperQuartile.EXPR.matrix"> + <data format="tabular" name="norm_UQ" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values"> <filter>additional_params['cross_sample_norm'] == "UpperQuartile"</filter> </data> + + <data format="tabular" name="norm_TMM_gene" label="${tool.name} on ${on_string}: matrix of TMM-normalized expression values"> + <filter>additional_params['cross_sample_norm'] == "TMM" and gene_trans_map</filter> + </data> + <data format="tabular" name="norm_UQ_gene" label="${tool.name} on ${on_string}: matrix of UpperQuartile-normalized expression values"> + <filter>additional_params['cross_sample_norm'] == "UpperQuartile" and gene_trans_map</filter> + </data> </outputs> <tests> <test> @@ -68,7 +108,7 @@ <has_n_columns n="3" /> </assert_contents> </output> - <output name="norm"> + <output name="norm_TMM"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> @@ -91,7 +131,7 @@ <has_n_columns n="3" /> </assert_contents> </output> - <output name="norm"> + <output name="norm_TMM"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> @@ -114,7 +154,7 @@ <has_n_columns n="3" /> </assert_contents> </output> - <output name="norm"> + <output name="norm_TMM"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> @@ -137,7 +177,7 @@ <has_n_columns n="3" /> </assert_contents> </output> - <output name="norm"> + <output name="norm_UQ"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> </assert_contents> @@ -193,7 +233,7 @@ <has_n_columns n="3" /> </assert_contents> </output> - <output name="norm"> + <output name="norm_TMM"> <assert_contents> <has_line_matching expression="TRINITY_DN3_c0_g1	.*" /> <has_n_columns n="3" /> |
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| diff -r 67906d99d3c0 -r 13ab393ba794 macros.xml --- a/macros.xml Mon Jan 22 11:28:19 2018 -0500 +++ b/macros.xml Thu Jun 14 03:12:12 2018 -0400 |
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| @@ -2,19 +2,19 @@ <macros> <xml name="requirements"> <requirements> - <requirement type="package" version="2.4.0">trinity</requirement> + <requirement type="package" version="2.6.6">trinity</requirement> <yield/> </requirements> </xml> - <token name="@WRAPPER_VERSION@">2.4.0</token> + <token name="@WRAPPER_VERSION@">2.6.6</token> <token name="@COMMAND_PAIRED_STRAND_JACCARD@"> - #if $inputs.strand.is_strand_specific: - --SS_lib_type $inputs.strand.library_type + #if $pool.inputs.strand.is_strand_specific: + --SS_lib_type $pool.inputs.strand.library_type #end if - $inputs.jaccard_clip + $pool.inputs.jaccard_clip </token> <xml name="input_paired_strand_jaccard"> |
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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/Trinity.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/Trinity.map Thu Jun 14 03:12:12 2018 -0400 |
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| @@ -0,0 +1,7 @@ +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 +TRINITY_DN2_c1_g1 TRINITY_DN2_c1_g1_i1 +TRINITY_DN2_c2_g1 TRINITY_DN2_c2_g1_i1 +TRINITY_DN2_c3_g1 TRINITY_DN2_c3_g1_i1 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 |
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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.DE.subset.GOseq.enriched --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.0.DE.subset.GOseq.enriched Thu Jun 14 03:12:12 2018 -0400 |
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| @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR |
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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/analyze_diff_expr/results.matrix --- a/test-data/count/analyze_diff_expr/results.matrix Mon Jan 22 11:28:19 2018 -0500 +++ b/test-data/count/analyze_diff_expr/results.matrix Thu Jun 14 03:12:12 2018 -0400 |
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| @@ -1,14 +1,14 @@ - wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR3788|c0_g1_i1 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00 TR24|c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 -TR4277|c0_g1_i1 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR3091|c0_g1_i1 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 TR2779|c0_g1_i1 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 -TR2672|c0_g1_i1 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00 -TR127|c1_g1_i1 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 TR2107|c1_g1_i1 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR4761|c0_g1_i1 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 TR5055|c0_g2_i1 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00 -TR3091|c0_g1_i1 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 -TR4761|c0_g1_i1 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR5075|c0_g1_i1 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00 +TR2672|c0_g1_i1 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00 +TR4277|c0_g1_i1 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR127|c1_g1_i1 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 TR131|c0_g1_i1 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 -TR5075|c0_g1_i1 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00 TR1894|c2_g1_i1 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00 -TR3788|c0_g1_i1 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00 |
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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/analyze_diff_expr/results.matrix.RData |
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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat --- a/test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat Mon Jan 22 11:28:19 2018 -0500 +++ b/test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat Thu Jun 14 03:12:12 2018 -0400 |
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| @@ -1,14 +1,14 @@ wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR3788|c0_g1_i1 -1.22775484082629 -0.443483531881724 -0.874117886211586 1.12588211378841 1.65760259323259 1.57960008123132 -0.353285722910146 -0.874117886211586 -0.590324920210995 TR24|c0_g1_i1 0.106533882165825 -0.313797916782532 0.025003996669227 -1.19180739240392 -1.23133575659056 -1.2719777410879 1.39963914188743 1.22079106142351 1.25695072471892 -TR4277|c0_g1_i1 3.24415794782388 3.31812623217364 3.18414689752048 -1.98611482817144 -1.80411699442855 -1.51461037723356 -1.44630436384266 -1.5322044372483 -1.46308007659348 +TR3091|c0_g1_i1 -2.42438780178849 -2.77802475640319 -2.62602166295814 1.02359379610527 1.32351327005887 1.20686835120661 1.43575453462855 1.4783149968566 1.36038927229391 TR2779|c0_g1_i1 -0.795433018475884 -1.23380302158535 -0.574143153586594 -1.13287411273457 -0.795433018475884 -0.712970858283911 1.74646076035339 1.75438767612502 1.74380874666379 -TR2672|c0_g1_i1 0.965440325233136 1.96544032523314 1.58211168568163 -2.94145027037538 -0.619522175488021 -1.35648776965423 0.965440325233136 -0.619522175488021 0.0585497296246169 -TR127|c1_g1_i1 1.25755965737847 2.52059406321227 2.02309440374145 -0.479405936787734 -2.06436843750889 -1.06436843750889 -0.0643684375088904 -1.06436843750889 -1.06436843750889 TR2107|c1_g1_i1 2.49178842221691 2.62929194596684 2.16986032732955 -0.607747251334006 -0.607747251334006 -0.41510217339161 -1.41510217339161 -2.41510217339161 -1.83013967267045 +TR4761|c0_g1_i1 2.06406810079911 1.80544476674762 1.90822498634624 -1.67981690730689 -1.51400801433681 -1.59017969482221 -0.339510283104669 -0.357888812419525 -0.296334141902888 TR5055|c0_g2_i1 1.90528891290538 0.865760548718745 1.50319046933404 -0.982236357836205 -0.304164452723568 -1.30416445272357 -0.982236357836205 -0.982236357836205 0.280798047997588 -TR3091|c0_g1_i1 -2.42438780178849 -2.77802475640319 -2.62602166295814 1.02359379610527 1.32351327005887 1.20686835120661 1.43575453462855 1.4783149968566 1.36038927229391 -TR4761|c0_g1_i1 2.06406810079911 1.80544476674762 1.90822498634624 -1.67981690730689 -1.51400801433681 -1.59017969482221 -0.339510283104669 -0.357888812419525 -0.296334141902888 +TR5075|c0_g1_i1 -1.04544737992556 -0.329240345926152 -0.393370683345868 -2.04544737992556 -1.68287730054085 -1.39337068334587 2.50474970263492 2.07793503557972 2.30706903479522 +TR2672|c0_g1_i1 0.965440325233136 1.96544032523314 1.58211168568163 -2.94145027037538 -0.619522175488021 -1.35648776965423 0.965440325233136 -0.619522175488021 0.0585497296246169 +TR4277|c0_g1_i1 3.24415794782388 3.31812623217364 3.18414689752048 -1.98611482817144 -1.80411699442855 -1.51461037723356 -1.44630436384266 -1.5322044372483 -1.46308007659348 +TR127|c1_g1_i1 1.25755965737847 2.52059406321227 2.02309440374145 -0.479405936787734 -2.06436843750889 -1.06436843750889 -0.0643684375088904 -1.06436843750889 -1.06436843750889 TR131|c0_g1_i1 -3.50802026981862 -3.6944333940495 -3.55241438917708 1.41625240401813 1.71671228997234 1.68718414007205 1.98577454287534 1.99158406095747 1.95736061514986 -TR5075|c0_g1_i1 -1.04544737992556 -0.329240345926152 -0.393370683345868 -2.04544737992556 -1.68287730054085 -1.39337068334587 2.50474970263492 2.07793503557972 2.30706903479522 TR1894|c2_g1_i1 2.11263053903627 1.56008951600749 1.23816142112012 -1.34680107960103 -0.761838578879876 0.238161421120124 -1.34680107960103 -0.346801079601032 -1.34680107960103 -TR3788|c0_g1_i1 -1.22775484082629 -0.443483531881724 -0.874117886211586 1.12588211378841 1.65760259323259 1.57960008123132 -0.353285722910146 -0.874117886211586 -0.590324920210995 |
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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf |
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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/analyze_diff_expr/results.matrix.log2.dat --- a/test-data/count/analyze_diff_expr/results.matrix.log2.dat Mon Jan 22 11:28:19 2018 -0500 +++ b/test-data/count/analyze_diff_expr/results.matrix.log2.dat Thu Jun 14 03:12:12 2018 -0400 |
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| @@ -1,14 +0,0 @@ -wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 -TR24|c0_g1_i1 6.5077946401987 6.08746284125034 6.4262647547021 5.20945336562895 5.16992500144231 5.12928301694497 7.8008998999203 7.62205181945638 7.65821148275179 -TR4277|c0_g1_i1 12.1250905393033 12.199058823653 12.0650794889999 6.89481776330794 7.07681559705083 7.36632221424582 7.43462822763672 7.34872815423108 7.4178525148859 -TR2779|c0_g1_i1 7.54689445988764 7.10852445677817 7.76818432477693 7.20945336562895 7.54689445988764 7.62935662007961 10.0887882387169 10.0967151544885 10.0861362250273 -TR2672|c0_g1_i1 3.90689059560852 4.90689059560852 4.52356195605701 0 2.32192809488736 1.58496250072116 3.90689059560852 2.32192809488736 3 -TR127|c1_g1_i1 3.32192809488736 4.58496250072116 4.08746284125034 1.58496250072116 0 1 2 1 1 -TR2107|c1_g1_i1 5.90689059560852 6.04439411935845 5.58496250072116 2.8073549220576 2.8073549220576 3 2 1 1.58496250072116 -TR5055|c0_g2_i1 5.20945336562895 4.16992500144231 4.8073549220576 2.32192809488736 3 2 2.32192809488736 2.32192809488736 3.58496250072116 -TR3091|c0_g1_i1 4.52356195605701 4.16992500144231 4.32192809488736 7.97154355395077 8.27146302790437 8.1548181090521 8.38370429247405 8.4262647547021 8.30833903013941 -TR4761|c0_g1_i1 11.0292872269682 10.7706638929168 10.8734441125154 7.28540221886225 7.45121111183233 7.37503943134692 8.62570884306447 8.60733031374961 8.66888498426625 -TR131|c0_g1_i1 5.04439411935845 4.85798099512757 5 9.96866679319521 10.2691266791494 10.2395985292491 10.5381889320524 10.5439984501345 10.5097750043269 -TR5075|c0_g1_i1 3.8073549220576 4.52356195605701 4.4594316186373 2.8073549220576 3.16992500144231 3.4594316186373 7.35755200461808 6.93073733756289 7.15987133677839 -TR1894|c2_g1_i1 4.4594316186373 3.90689059560852 3.58496250072116 1 1.58496250072116 2.58496250072116 1 2 1 -TR3788|c0_g1_i1 4.16992500144231 4.95419631038687 4.52356195605701 6.52356195605701 7.05528243550119 6.97727992349992 5.04439411935845 4.52356195605701 4.8073549220576 |
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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat --- a/test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat Mon Jan 22 11:28:19 2018 -0500 +++ b/test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -1,10 +0,0 @@ -wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 -wt_37_2 1 0.968650822800566 0.985499030254524 0.457364683078012 0.443497697874748 0.451451348748615 0.41961787977306 0.444203836374748 0.448348619980356 -wt_37_3 0.968650822800566 1 0.98879028662025 0.400031307625771 0.378330685571456 0.396636302989378 0.39057945325073 0.383299487197462 0.388022080096891 -wt_37_1 0.985499030254524 0.98879028662025 1 0.452638132682111 0.434834315692609 0.44176483058741 0.461437515072935 0.462172448553839 0.473652431554024 -wt_GSNO_3 0.457364683078012 0.400031307625771 0.452638132682111 1 0.965144031362199 0.979742518682039 0.844139129634192 0.862862111399854 0.857171072391268 -wt_GSNO_1 0.443497697874748 0.378330685571456 0.434834315692609 0.965144031362199 1 0.983818328020852 0.858668155107621 0.871693931267863 0.876908826664397 -wt_GSNO_2 0.451451348748615 0.396636302989378 0.44176483058741 0.979742518682039 0.983818328020852 1 0.854388461031158 0.878292745544781 0.861156659158544 -wt_ph8_3 0.41961787977306 0.39057945325073 0.461437515072935 0.844139129634192 0.858668155107621 0.854388461031158 1 0.984071267766826 0.98764423106737 -wt_ph8_1 0.444203836374748 0.383299487197462 0.462172448553839 0.862862111399854 0.871693931267863 0.878292745544781 0.984071267766826 1 0.989191009161984 -wt_ph8_2 0.448348619980356 0.388022080096891 0.473652431554024 0.857171072391268 0.876908826664397 0.861156659158544 0.98764423106737 0.989191009161984 1 |
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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf |
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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/contig_exn50_statistic/ExN50.stats --- a/test-data/count/contig_exn50_statistic/ExN50.stats Mon Jan 22 11:28:19 2018 -0500 +++ b/test-data/count/contig_exn50_statistic/ExN50.stats Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -1,5 +1,4 @@ -#E min_expr E-N50 num_transcripts -E33 525311.050 541 1 -E67 525311.050 541 2 -E99 329523.810 380 3 -E100 0 279 7 +Ex ExN50 num_transcripts +33 541 1 +67 541 2 +100 279 7 |
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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/define_clusters_by_cutting_tree/my_cluster_plots.pdf |
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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Mon Jan 22 11:28:19 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results Thu Jun 14 03:12:12 2018 -0400 |
| b |
| b'@@ -1,38 +1,38 @@\n sampleA\tsampleB\tbaseMeanA\tbaseMeanB\tbaseMean\tlog2FoldChange\tlfcSE\tstat\tpvalue\tpadj\n-TR4277|c0_g1_i1\twt_37\twt_GSNO\t3852.97388871986\t161.116814813422\t2007.04535176664\t4.57260002898197\t0.121471586836965\t37.6433711623376\t0\t0\n-TR131|c0_g1_i1\twt_37\twt_GSNO\t26.1866396538608\t1340.30918254958\t683.247911101723\t-5.67373033438939\t0.187375754459626\t-30.2799599166492\t2.10486694333775e-201\t3.89400384517483e-200\n-TR4761|c0_g1_i1\twt_37\twt_GSNO\t1645.20640957447\t193.196157329029\t919.201283451752\t3.08848040390227\t0.143569117275296\t21.5121501233448\t1.19819880470067e-102\t1.47777852579749e-101\n-TR3091|c0_g1_i1\twt_37\twt_GSNO\t16.7444693227929\t328.569936894811\t172.657203108802\t-4.29037251456992\t0.240582794801874\t-17.8332474610379\t3.90090325510546e-71\t3.60833551097255e-70\n-TR3638|c0_g1_i1\twt_37\twt_GSNO\t583.00358519031\t183.754416330029\t383.37900076017\t1.66018954854466\t0.144513974558734\t11.4880900176883\t1.51422805973163e-30\t1.12052876420141e-29\n-TR2487|c0_g1_i1\twt_37\twt_GSNO\t342.210853400436\t920.407318992504\t631.30908619647\t-1.42691086642688\t0.124648977132644\t-11.4474334186348\t2.42211055832184e-30\t1.49363484429847e-29\n-TR3788|c0_g1_i1\twt_37\twt_GSNO\t19.5075441237117\t134.95369713876\t77.2306206312357\t-2.77036684869735\t0.263152237265066\t-10.527620351967\t6.4442989603998e-26\t3.40627230763989e-25\n-TR1479|c0_g1_i1\twt_37\twt_GSNO\t129.593534475689\t371.064629188207\t250.329081831948\t-1.51441062491813\t0.145530800926874\t-10.4061175728641\t2.32511621828936e-25\t1.07536625095883e-24\n-TR2107|c1_g1_i1\twt_37\twt_GSNO\t48.9228907410258\t7.40521775805688\t28.1640542495414\t2.69488884014666\t0.432209832999676\t6.23514005094067\t4.51374085119887e-10\t1.85564901660398e-09\n-TR3854|c0_g1_i1\twt_37\twt_GSNO\t1573.69549271337\t2374.56159860719\t1974.12854566028\t-0.593515573382884\t0.111170659243154\t-5.33877893163104\t9.35746583039244e-08\t3.4622623572452e-07\n-TR2122|c0_g2_i2\twt_37\twt_GSNO\t119.534640490118\t199.143666337033\t159.339153413576\t-0.738644008220832\t0.168659021315898\t-4.37951081690053\t1.18946017688789e-05\t4.00091150407745e-05\n-TR1449|c0_g1_i1\twt_37\twt_GSNO\t180.814952011467\t104.755290736358\t142.785121373912\t0.784193680180578\t0.186004942516637\t4.21598302480827\t2.48692468039376e-05\t7.49709472786912e-05\n-TR4163|c0_g1_i1\twt_37\twt_GSNO\t347.283468916919\t232.772947466212\t290.028208191566\t0.576743600823335\t0.13722219355458\t4.20299068163444\t2.63411436384591e-05\t7.49709472786912e-05\n-TR2672|c0_g1_i1\twt_37\twt_GSNO\t18.3155337236093\t2.26581902751323\t10.2906763755613\t2.88788179640237\t0.725539563189254\t3.98032298019437\t6.88216980025882e-05\t0.000181885916149697\n-TR127|c1_g1_i1\twt_37\twt_GSNO\t13.461799216177\t1.21881296083961\t7.34030608850831\t3.33150202228086\t0.915899815581865\t3.63740877070095\t0.000275394687501815\t0.000667511143840185\n-TR5055|c0_g2_i1\twt_37\twt_GSNO\t23.3590211688541\t5.52768338415684\t14.4433522765055\t2.04460941512382\t0.563987307210913\t3.62527558507482\t0.000288653467606567\t0.000667511143840185\n-TR2844|c0_g1_i1\twt_37\twt_GSNO\t158.206282615139\t231.762548186068\t194.984415400603\t-0.550639207704626\t0.154913717539885\t-3.55448966333699\t0.000378713397971402\t0.000824258572055403\n-TR5212|c0_g1_i1\twt_37\twt_GSNO\t65.7079302129484\t107.875371765755\t86.7916509893515\t-0.713874873222434\t0.210087143945163\t-3.39799408862815\t0.000678818868686303\t0.00139534989674407\n-TR1894|c2_g1_i1\twt_37\twt_GSNO\t13.3497721959996\t2.96749216411516\t8.15863218005739\t2.04972102673103\t0.716146945354672\t2.86215146210796\t0.00420775772107294\t0.00819405450945783\n-TR24|c0_g1_i1\twt_37\twt_GSNO\t69.9065207344592\t41.2394742844514\t55.5729975094553\t0.760351613917761\t0.269735390145923\t2.81887969356346\t0.00481915767774413\t0.00891544170382664\n-TR2779|c0_g1_i1\twt_37\twt_GSNO\t155.915506826481\t205.619872596257\t180.767689711369\t-0.402350189521528\t0.18910416680051\t-2.12766432558821\t0.0333649247395808\t0.0587858197792614\n-TR3807|c0_g1_i1\twt_37\twt_GSNO\t3.48709246029019\t0.350050334268211\t1.9185713972792\t2.6523001983829\t1.38324824664578\t1.91744338358239\t0.055181627150862\t0.092164962039527\n-TR1492|c0_g1_i2\twt_37\twt_GSNO\t1640.89375005483\t1435.648932614'..b'10.2906763755613\t2.9857084616452\t0.761209385049731\t3.92232218924907\t8.76996107235725e-05\t0.000206720510991278\n+TR5055|c0_g2_i1\twt_37\twt_GSNO\t23.3590211688541\t5.52768338415684\t14.4433522765055\t2.08513896568298\t0.577312677901881\t3.61180179389265\t0.00030407694239889\t0.000668969273277559\n+TR2844|c0_g1_i1\twt_37\twt_GSNO\t158.206282615139\t231.762548186068\t194.984415400603\t-0.551426184671915\t0.155135532159318\t-3.55448024702441\t0.000378726959348647\t0.000781124353656584\n+TR127|c1_g1_i1\twt_37\twt_GSNO\t13.461799216177\t1.21881296083961\t7.34030608850831\t3.52517488060096\t1.00261297574214\t3.51598769005717\t0.00043812129728732\t0.000850470753557739\n+TR5212|c0_g1_i1\twt_37\twt_GSNO\t65.7079302129484\t107.875371765755\t86.7916509893515\t-0.715754705745061\t0.210644233010842\t-3.39793164766215\t0.000678973819799399\t0.0012447853362989\n+TR1894|c2_g1_i1\twt_37\twt_GSNO\t13.3497721959996\t2.96749216411516\t8.15863218005739\t2.116499695166\t0.744618031030184\t2.84239651333424\t0.00447757649596373\t0.00777684338772647\n+TR24|c0_g1_i1\twt_37\twt_GSNO\t69.9065207344592\t41.2394742844514\t55.5729975094553\t0.763675526543044\t0.270944643994893\t2.81856660933825\t0.00482386011442888\t0.00795936918880766\n+TR4669|c0_g2_i1\twt_37\twt_GSNO\t0\t167.096667347181\t83.5483336735905\t-10.0466852501689\t3.90738405199054\t-2.57120495873725\t0.0101345328521317\t0.0159256944819212\n+TR2779|c0_g1_i1\twt_37\twt_GSNO\t155.915506826481\t205.619872596257\t180.767689711369\t-0.403209397282846\t0.18950756245476\t-2.12766916559914\t0.033364523163095\t0.0500467847446426\n+TR3807|c0_g1_i1\twt_37\twt_GSNO\t3.48709246029019\t0.350050334268211\t1.9185713972792\t3.04810928058763\t1.5874506366217\t1.92012854464212\t0.0548416645360559\t0.0786858665082542\n+TR1492|c0_g1_i2\twt_37\twt_GSNO\t1640.89375005483\t1435.64893261411\t1538.27134133447\t0.192601921423703\t0.101311986688049\t1.90107733270247\t0.0572918841322824\t0.0787763406818883\n+TR4084|c0_g1_i1\twt_37\twt_GSNO\t93.2264707954139\t121.352438036668\t107.289454416041\t-0.381231151484282\t0.21399248813321\t-1.78151651401411\t0.0748281095286258\t0.0987731045777861\n+TR1891|c0_g1_i1\twt_37\twt_GSNO\t107.628573623499\t135.399287466928\t121.513930545214\t-0.329513668205708\t0.189733845104182\t-1.7367152814764\t0.0824374390602291\t0.104632134191829\n+TR1837|c2_g1_i1\twt_37\twt_GSNO\t0.308903905435236\t2.22601224010275\t1.26745807276899\t-2.87715913917267\t1.7927876855897\t-1.60485213184979\t0.108526350064413\t1\n+TR5075|c0_g1_i1\twt_37\twt_GSNO\t15.8633018853512\t9.23822794034992\t12.5507649128506\t0.776103293030194\t0.516446682273215\t1.5027752518693\t0.13289700980576\t0.16070937436521\n+TR4859|c0_g1_i1\twt_37\twt_GSNO\t7.32690480813971\t3.17910584569163\t5.25300532691567\t1.23041974278822\t0.82607009598701\t1.48948587869905\t0.13635946915836\t0.16070937436521\n+TR939|c0_g1_i1\twt_37\twt_GSNO\t84.2568220960088\t96.9171174594069\t90.5869697777078\t-0.203187486812458\t0.203052234052517\t-1.00066609835923\t0.316988262617008\t0.354139456794138\n+TR2278|c0_g1_i1\twt_37\twt_GSNO\t486.5272515724\t448.140178813055\t467.333715192727\t0.118924512672215\t0.120068895863502\t0.990468945491189\t0.321944960721944\t0.354139456794138\n+TR2011|c5_g1_i1\twt_37\twt_GSNO\t5.60408627995835\t7.88255079488408\t6.74331853742122\t-0.50342873702063\t0.712267625142964\t-0.706797163383052\t0.479692537619295\t0.510640443272153\n+TR2182|c3_g2_i6\twt_37\twt_GSNO\t2.24974854180929\t1.3031439398571\t1.77644624083319\t0.878491642458712\t1.45214866443311\t0.604959852923637\t0.545205672528741\t0.562243349795264\n+TR3249|c0_g1_i1\twt_37\twt_GSNO\t1.12573841927462\t2.128954842887\t1.62734663108081\t-0.858277190977929\t1.45820967054459\t-0.588582841216099\t0.556141147160533\t1\n+TR1678|c0_g1_i1\twt_37\twt_GSNO\t0.595141051681226\t0.700100668536423\t0.647620860108824\t-0.322353878735801\t2.26929239960538\t-0.142050393678601\t0.887040200834538\t1\n+TR1122|c0_g1_i1\twt_37\twt_GSNO\t1.41370386226057\t1.3031439398571\t1.35842390105883\t0.189589394350501\t1.67633508161709\t0.113097552171736\t0.909953215626095\t1\n+TR1982|c2_g1_i1\twt_37\twt_GSNO\t5.73684100209948\t5.71221669652109\t5.72452884931028\t-0.0104554076697487\t0.738553450989727\t-0.0141566025529196\t0.988705042660126\t0.988705042660126\n' 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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -0,0 +1,7 @@ +sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR4277|c0_g1_i1 wt_37 wt_GSNO 3852.97388871986 161.116814813422 2007.04535176664 4.57260002898197 0.121471586836965 37.6433711623376 0 0 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR4761|c0_g1_i1 wt_37 wt_GSNO 1645.20640957447 193.196157329029 919.201283451752 3.08848040390227 0.143569117275296 21.5121501233448 1.19819880470067e-102 1.47777852579749e-101 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR2107|c1_g1_i1 wt_37 wt_GSNO 48.9228907410258 7.40521775805688 28.1640542495414 2.69488884014666 0.432209832999676 6.23514005094067 4.51374085119887e-10 1.85564901660398e-09 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR2672|c0_g1_i1 wt_37 wt_GSNO 18.3155337236093 2.26581902751323 10.2906763755613 2.88788179640237 0.725539563189254 3.98032298019437 6.88216980025882e-05 0.000181885916149697 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00 +TR127|c1_g1_i1 wt_37 wt_GSNO 13.461799216177 1.21881296083961 7.34030608850831 3.33150202228086 0.915899815581865 3.63740877070095 0.000275394687501815 0.000667511143840185 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR5055|c0_g2_i1 wt_37 wt_GSNO 23.3590211688541 5.52768338415684 14.4433522765055 2.04460941512382 0.563987307210913 3.62527558507482 0.000288653467606567 0.000667511143840185 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00 |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -0,0 +1,4 @@ +sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR131|c0_g1_i1 wt_37 wt_GSNO 26.1866396538608 1340.30918254958 683.247911101723 -5.67373033438939 0.187375754459626 -30.2799599166492 2.10486694333775e-201 3.89400384517483e-200 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR3091|c0_g1_i1 wt_37 wt_GSNO 16.7444693227929 328.569936894811 172.657203108802 -4.29037251456992 0.240582794801874 -17.8332474610379 3.90090325510546e-71 3.60833551097255e-70 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR3788|c0_g1_i1 wt_37 wt_GSNO 19.5075441237117 134.95369713876 77.2306206312357 -2.77036684869735 0.263152237265066 -10.527620351967 6.4442989603998e-26 3.40627230763989e-25 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00 |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results Mon Jan 22 11:28:19 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -1,39 +1,38 @@ -logFC logCPM PValue FDR -TR131|c0_g1_i1 5.8364197685119 16.0402624962907 0 0 -TR4277|c0_g1_i1 -4.41329137350676 17.4523259866001 0 0 -TR3091|c0_g1_i1 4.45193883524837 14.0450613692144 2.75977672027703e-191 3.0023764016608e-190 -TR4761|c0_g1_i1 -2.92753980838104 16.3343761538543 3.16039621227453e-191 3.0023764016608e-190 -TR2487|c0_g1_i1 1.58705373680526 15.8895982491351 1.69098562804069e-123 1.28514907731092e-122 -TR1479|c0_g1_i1 1.67068054401246 14.5625418524933 4.82942248775202e-81 3.05863424224295e-80 -TR3638|c0_g1_i1 -1.49936398500381 15.1049693447894 1.31792237756209e-64 7.15443576390849e-64 -TR3854|c0_g1_i1 0.756865722480515 17.5147652035186 8.35417282711821e-40 3.96823209288115e-39 -TR2122|c0_g2_i2 0.903942128151819 13.8996874045924 3.62505920095794e-13 1.53058055151558e-12 -TR2844|c0_g1_i1 0.707836713891037 14.1854217777842 1.87464339893047e-12 7.1236449159358e-12 -TR3788|c0_g1_i1 2.92403132462783 12.8779140660683 1.50355808369265e-09 5.19410974366551e-09 -TR4669|c0_g2_i1 10.5374101870061 13.0322839834498 3.83881845042015e-08 1.21562584263305e-07 -TR2672|c0_g1_i1 -2.77697626464917 10.2324144831548 6.6653206315345e-08 1.9483244922947e-07 -TR4163|c0_g1_i1 -0.420124679057253 14.7293558096347 2.6407759845512e-06 7.16782052949613e-06 -TR2107|c1_g1_i1 -2.54740509831049 11.4796217709789 1.31520100526586e-05 3.33184254667352e-05 -TR2779|c0_g1_i1 0.57151150266807 14.0680960027645 7.44562831370785e-05 0.000176833672450561 -TR127|c1_g1_i1 -3.25307512484374 9.84850588284066 0.000331345441643876 0.000740654516615722 -TR1894|c2_g1_i1 -1.90241917506329 9.93135664117576 0.00432077639530722 0.00912163905675968 -TR5055|c0_g2_i1 -1.8950478385132 10.598211984773 0.00591755208579545 0.0118351041715909 -TR2090|c0_g1_i1 6.41050251489574 9.11635750687386 0.0113096900461153 0.021488411087619 -TR5212|c0_g1_i1 0.867439938079617 13.0331405503531 0.0317111501604761 0.0573820812427663 -TR3807|c0_g1_i1 -2.67963301995355 8.56046890206839 0.0557212159288941 0.0962457366044534 -TR1449|c0_g1_i1 -0.636836241811875 13.7146214195087 0.0845994280568489 0.139772968093924 -TR4084|c0_g1_i1 0.527023803952886 13.333880353991 0.19596368831627 0.301997237380275 -TR1891|c0_g1_i1 0.481345196849859 13.5019985083809 0.198682393013339 0.301997237380275 -TR24|c0_g1_i1 -0.590671163985234 12.3854267629296 0.21115333494008 0.308608720297039 -TR1837|c2_g1_i1 2.67943439258847 8.19914223144978 0.242162966500684 0.336820885113627 -TR4859|c0_g1_i1 -1.04273446956489 9.43870802835889 0.248183810083725 0.336820885113627 -TR939|c0_g1_i1 0.361607908864682 13.0838256643577 0.341542524228359 0.447538480023367 -TR2011|c5_g1_i1 0.672074276530526 9.63297397547156 0.357699118838244 0.453085550528442 -TR5075|c0_g1_i1 -0.617596452044795 10.4317228965746 0.378826401739151 0.464367847293153 -TR3249|c0_g1_i1 0.936067544593607 8.34110243846743 0.532174466327564 0.631957178763983 -TR1492|c0_g1_i2 -0.0311770185465736 17.1360846492483 0.562063331952301 0.647224442854165 -TR2278|c0_g1_i1 0.0373157391528861 15.4251088322423 0.63557189922311 0.710345063837593 -TR2182|c3_g2_i6 -0.665499179094881 8.45651702709919 0.835363486459349 0.906966071013008 -TR1982|c2_g1_i1 0.176241441184615 9.49445846907393 0.904611213246767 0.954867391760477 -TR1678|c0_g1_i1 0.476522568809639 7.93710096737952 1 1 -TR1122|c0_g1_i1 -0.015204817268041 8.26206767263358 1 1 +sampleA sampleB logFC logCPM PValue FDR +TR131|c0_g1_i1 wt_37 wt_GSNO -5.83641794955382 16.0393491449056 0 0 +TR4277|c0_g1_i1 wt_37 wt_GSNO 4.41329536892161 17.453649857324 0 0 +TR3091|c0_g1_i1 wt_37 wt_GSNO -4.45192710783926 14.0403115023365 4.66239713643175e-192 5.75028980159916e-191 +TR4761|c0_g1_i1 wt_37 wt_GSNO 2.92754337500687 16.3361488759619 3.05265683396309e-191 2.82370757141586e-190 +TR2487|c0_g1_i1 wt_37 wt_GSNO -1.58705168340508 15.8893887856701 9.57106937146597e-124 7.08259133488482e-123 +TR1479|c0_g1_i1 wt_37 wt_GSNO -1.67065982572176 14.5610246448295 4.39649357092684e-84 2.71117103540489e-83 +TR3638|c0_g1_i1 wt_37 wt_GSNO 1.49937182627392 15.1071990563814 1.60652562072048e-64 8.49163542380826e-64 +TR3854|c0_g1_i1 wt_37 wt_GSNO -0.756864683109858 17.5153338325952 9.14141417630157e-40 4.22790405653948e-39 +TR2122|c0_g2_i2 wt_37 wt_GSNO -0.90394318029981 13.8984589155106 3.98287653266084e-13 1.63740479676057e-12 +TR2844|c0_g1_i1 wt_37 wt_GSNO -0.707834005847516 14.1849675326065 1.90004997002049e-12 7.0301848890758e-12 +TR3788|c0_g1_i1 wt_37 wt_GSNO -2.92402824575823 12.8707284018497 1.35908019280542e-09 4.57145155761824e-09 +TR4669|c0_g2_i1 wt_37 wt_GSNO -10.5373989771184 13.0207784411552 2.87822490296537e-08 8.87452678414323e-08 +TR2672|c0_g1_i1 wt_37 wt_GSNO 2.77705541360002 10.2430402179839 7.41806563943484e-08 2.11129560506992e-07 +TR4163|c0_g1_i1 wt_37 wt_GSNO 0.420123134789911 14.7306522277754 2.74345107938324e-06 7.25054928122714e-06 +TR127|c1_g1_i1 wt_37 wt_GSNO 3.26487561187968 9.85808314705506 6.1191913603037e-06 1.50940053554158e-05 +TR2107|c1_g1_i1 wt_37 wt_GSNO 2.54741701164587 11.489948731934 1.24782096095324e-05 2.88558597220436e-05 +TR2779|c0_g1_i1 wt_37 wt_GSNO -0.571512278204146 14.0677635717422 7.39487278515011e-05 0.000160947231206208 +TR1894|c2_g1_i1 wt_37 wt_GSNO 1.88989717290856 9.93884262525918 0.00064827406279645 0.00133256335130381 +TR5055|c0_g2_i1 wt_37 wt_GSNO 1.89504810994952 10.6064804346292 0.00584438080176016 0.011381162613954 +TR3807|c0_g1_i1 wt_37 wt_GSNO 2.66606066906632 8.56455983886691 0.0188051214716541 0.0347894747225602 +TR5212|c0_g1_i1 wt_37 wt_GSNO -0.867441722907523 13.0312878134755 0.0313380642877521 0.055214684697468 +TR1449|c0_g1_i1 wt_37 wt_GSNO 0.636828244112651 13.716963541734 0.0836258106887223 0.140643408885578 +TR1837|c2_g1_i1 wt_37 wt_GSNO -2.70136949048315 8.19724487849862 0.11443273811818 0.184087448277072 +TR4859|c0_g1_i1 wt_37 wt_GSNO 1.06021338602227 9.44252758756623 0.17021260004507 0.262411091736149 +TR4084|c0_g1_i1 wt_37 wt_GSNO -0.527027354857722 13.3333941866224 0.195100037539558 0.280916147575458 +TR1891|c0_g1_i1 wt_37 wt_GSNO -0.481344817930584 13.5015018099629 0.197400536134106 0.280916147575458 +TR24|c0_g1_i1 wt_37 wt_GSNO 0.590686928315332 12.3882336221811 0.209814398393357 0.287523434835341 +TR2011|c5_g1_i1 wt_37 wt_GSNO -0.668008806764204 9.63014074618193 0.239244885423374 0.316145027166602 +TR939|c0_g1_i1 wt_37 wt_GSNO -0.361607139894815 13.0833886152319 0.340252678428006 0.434115486270215 +TR5075|c0_g1_i1 wt_37 wt_GSNO 0.617585416067661 10.4358029661318 0.377913209145196 0.466092957945741 +TR1492|c0_g1_i2 wt_37 wt_GSNO 0.0311900896664335 17.1368189470585 0.559289231968699 0.657620159615942 +TR3249|c0_g1_i1 wt_37 wt_GSNO -0.894241538356016 8.33957569586088 0.568752570478653 0.657620159615942 +TR2278|c0_g1_i1 wt_37 wt_GSNO -0.0373200220187202 15.4258149088647 0.636489077475997 0.713639268685208 +TR2182|c3_g2_i6 wt_37 wt_GSNO 0.714549920613349 8.45775163335771 0.790296098133788 0.860028106792652 +TR1982|c2_g1_i1 wt_37 wt_GSNO -0.181275971858276 9.49467590956657 0.873422282667325 0.923332127391172 +TR1678|c0_g1_i1 wt_37 wt_GSNO -0.476606391142577 7.93769527756871 1 1 +TR1122|c0_g1_i1 wt_37 wt_GSNO 0.0647357997613641 8.26206759454538 1 1 |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf |
| b |
| Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.edgeR.DE_results.MA_n_Volcano.pdf has changed |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results Mon Jan 22 11:28:19 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -1,39 +1,38 @@ -logFC logCPM PValue FDR -TR131|c0_g1_i1 5.8235943392439 16.1127963113785 7.14846919291531e-10 2.71641829330782e-08 -TR4277|c0_g1_i1 -4.41182125975734 17.3835558041266 1.56187740933885e-09 2.96756707774382e-08 -TR3091|c0_g1_i1 4.43711915085412 14.1189484156579 4.80332538807657e-08 5.96619459206176e-07 -TR2487|c0_g1_i1 1.58597331690052 15.926957585609 6.28020483374923e-08 5.96619459206176e-07 -TR4761|c0_g1_i1 -2.92047098366841 16.2714320125634 5.50582910815067e-07 4.18443012219451e-06 -TR1479|c0_g1_i1 1.67737907773679 14.6004783880878 9.51214752241748e-07 5.52604916020242e-06 -TR3638|c0_g1_i1 -1.50273266496817 15.0596817330556 1.02518921423282e-06 5.52604916020242e-06 -TR3788|c0_g1_i1 2.93902285611693 12.9382150715361 2.41689084349911e-06 1.02046502281074e-05 -TR3854|c0_g1_i1 0.759398996973938 17.5343629610585 1.16337877056893e-06 5.52604916020242e-06 -TR2107|c1_g1_i1 -2.46238704341773 11.2600018185657 0.000160625103091043 0.000554886719769058 -TR2122|c0_g2_i2 0.898555189960494 13.9141616710754 0.000116065228333624 0.000441047867667773 -TR2844|c0_g1_i1 0.712285451514242 14.1964395706942 0.000226456956836179 0.0007171136966479 -TR5212|c0_g1_i1 0.877383155201317 13.0382243238454 0.00044264831250554 0.00129389506732389 -TR4163|c0_g1_i1 -0.417753044994067 14.7100536369854 0.00073550773195026 0.00199637812957928 -TR1449|c0_g1_i1 -0.639430683731338 13.6750299459863 0.0021688744394372 0.00549448191324091 -TR2672|c0_g1_i1 -2.89090970573392 9.81450205355949 0.0110308904582196 0.0220617809164392 -TR127|c1_g1_i1 -3.10441694967501 9.33201892428652 0.0147505107490706 0.0271381068158418 -TR939|c0_g1_i1 0.363392391144623 13.0700139113805 0.00528218330196852 0.0125451853421752 -TR5055|c0_g2_i1 -1.80082179647401 10.290740057161 0.014997374819281 0.0271381068158418 -TR1894|c2_g1_i1 -1.81920882927282 9.4761161835092 0.0211021355265418 0.0348643978264604 -TR1891|c0_g1_i1 0.477106166889499 13.4994625375761 0.00640932243854848 0.0143267207449907 -TR1837|c2_g1_i1 2.21852868850051 7.02301103616459 0.041457300582048 0.063015096884713 -TR3807|c0_g1_i1 -1.9168529396959 7.35599058475032 0.0566225608328877 0.0827560504480666 -TR2779|c0_g1_i1 0.600059279980753 14.0739938889057 0.00964636468216327 0.0203645476623447 -TR24|c0_g1_i1 -0.588697529952342 12.3096839182028 0.0194904179372949 0.0336652673462366 -TR4859|c0_g1_i1 -1.06821251099455 8.91301871295058 0.111617387620425 0.157091138132451 -TR2090|c0_g1_i1 2.22339391910091 8.98366602727699 0.254495907488744 0.322361482819076 -TR4084|c0_g1_i1 0.567566096899832 13.3297126444574 0.036433281659912 0.0576860292948607 -TR2182|c3_g2_i6 -1.0316496616205 7.37334712818428 0.34572838664377 0.423796086853654 -TR2011|c5_g1_i1 0.791574287810665 9.32879226678442 0.161547389819689 0.211682786660282 -TR5075|c0_g1_i1 -0.550289601556128 10.1785868671389 0.12853444928267 0.174439609740767 -TR1678|c0_g1_i1 0.331221243897688 5.95523974949609 0.7547763751788 0.806418050624271 -TR4669|c0_g2_i1 6.27373933776222 13.1239272719772 0.48073138273468 0.553569471027814 -TR1122|c0_g1_i1 -0.199192308627843 7.01379133029712 0.87736931102229 0.87736931102229 -TR3249|c0_g1_i1 0.258869539778469 7.31927198802943 0.798677928444158 0.820263818402108 -TR1982|c2_g1_i1 0.132112224684827 9.08491674138301 0.763974995328257 0.806418050624271 -TR2278|c0_g1_i1 0.0407550618622219 15.423513715505 0.613273487399665 0.685423309446684 -TR1492|c0_g1_i2 -0.0324123498367541 17.1356104672946 0.389074079094509 0.462025468924729 +sampleA sampleB logFC logCPM PValue FDR +TR131|c0_g1_i1 wt_37 wt_GSNO -5.82360148900389 16.1142242655408 6.54502972918692e-10 2.42166099979916e-08 +TR4277|c0_g1_i1 wt_37 wt_GSNO 4.41183386172098 17.3836256000268 1.7102544921365e-09 3.16397081045253e-08 +TR3091|c0_g1_i1 wt_37 wt_GSNO -4.43700179801176 14.1203688767724 4.42033048679943e-08 5.45174093371929e-07 +TR2487|c0_g1_i1 wt_37 wt_GSNO -1.58598083708684 15.9280757073272 7.01720228399608e-08 6.49091211269637e-07 +TR4761|c0_g1_i1 wt_37 wt_GSNO 2.92043321768346 16.2716301848411 5.72725934421127e-07 4.23817191471634e-06 +TR1479|c0_g1_i1 wt_37 wt_GSNO -1.67738254434993 14.6016057367881 1.03919750932427e-06 5.8615543150164e-06 +TR3638|c0_g1_i1 wt_37 wt_GSNO 1.50288215872986 15.0600281889274 1.12469315856867e-06 5.8615543150164e-06 +TR3788|c0_g1_i1 wt_37 wt_GSNO -2.93907650045598 12.9393872783943 2.35975448958169e-06 9.70121290161359e-06 +TR3854|c0_g1_i1 wt_37 wt_GSNO -0.759397690410038 17.5353083640786 1.26736309513868e-06 5.8615543150164e-06 +TR2107|c1_g1_i1 wt_37 wt_GSNO 2.46233758474327 11.260249244859 0.000163907571391062 0.000551325467406299 +TR2122|c0_g2_i2 wt_37 wt_GSNO -0.898543060702643 13.9151768182402 0.000124408949544541 0.000460313113314803 +TR2844|c0_g1_i1 wt_37 wt_GSNO -0.712202725875737 14.1973066750225 0.000243984033514546 0.000752284103336518 +TR5212|c0_g1_i1 wt_37 wt_GSNO -0.87701850957337 13.0391017777502 0.000473838954429694 0.00134861856260759 +TR4163|c0_g1_i1 wt_37 wt_GSNO 0.417694804483349 14.7107025605232 0.000805848497363634 0.00212974245731817 +TR2672|c0_g1_i1 wt_37 wt_GSNO 2.90562993555483 9.81450205355949 0.00822748279906008 0.0169120479758457 +TR1449|c0_g1_i1 wt_37 wt_GSNO 0.640011354440497 13.6755402195434 0.00227354555819909 0.00560807904355776 +TR127|c1_g1_i1 wt_37 wt_GSNO 3.09466453837236 9.33233275488244 0.00997545255499303 0.0184545872267371 +TR1894|c2_g1_i1 wt_37 wt_GSNO 1.8273232048322 9.47625819175118 0.0170307015491222 0.0286425435144327 +TR5055|c0_g2_i1 wt_37 wt_GSNO 1.79897959483123 10.2910629958573 0.0144290410083875 0.025422596062397 +TR939|c0_g1_i1 wt_37 wt_GSNO -0.363394684962815 13.0708604932728 0.00579686595094712 0.0134052525115652 +TR1837|c2_g1_i1 wt_37 wt_GSNO -2.21418127698954 7.02378849272624 0.0306005987832276 0.0471759231241425 +TR1891|c0_g1_i1 wt_37 wt_GSNO -0.477062796219233 13.500309435849 0.00675073796972544 0.0146927826399907 +TR3807|c0_g1_i1 wt_37 wt_GSNO 1.91879773659378 7.35599058475032 0.0402625583382777 0.0572967176352414 +TR2779|c0_g1_i1 wt_37 wt_GSNO -0.600036558858359 14.0748557225205 0.00991998269314111 0.0184545872267371 +TR24|c0_g1_i1 wt_37 wt_GSNO 0.588796779058576 12.310400953631 0.0185008090691583 0.0297621711112546 +TR4859|c0_g1_i1 wt_37 wt_GSNO 1.06036244689068 8.9138577436531 0.104550838513832 0.143273371296733 +TR4084|c0_g1_i1 wt_37 wt_GSNO -0.567278869966665 13.330468891507 0.0372234219214301 0.0550906644437166 +TR2011|c5_g1_i1 wt_37 wt_GSNO -0.789577978066661 9.33004998835934 0.161975973261362 0.206659000367944 +TR2182|c3_g2_i6 wt_37 wt_GSNO 1.02218394394404 7.37517597546907 0.329234058043314 0.406055338253421 +TR5075|c0_g1_i1 wt_37 wt_GSNO 0.549449880041588 10.1791103984097 0.127566698813275 0.168570280574684 +TR4669|c0_g2_i1 wt_37 wt_GSNO -6.27345157840298 13.126293325041 0.423017017822531 0.489113426857301 +TR1678|c0_g1_i1 wt_37 wt_GSNO -0.330222398445961 5.95523974949609 0.735881722270124 0.79829094077818 +TR1122|c0_g1_i1 wt_37 wt_GSNO 0.193564460109425 7.01613737702005 0.875819231521416 0.875819231521416 +TR3249|c0_g1_i1 wt_37 wt_GSNO -0.276543877903423 7.32180296800742 0.776715509946338 0.79829094077818 +TR1982|c2_g1_i1 wt_37 wt_GSNO -0.131251756802268 9.08566155151058 0.763275890632561 0.79829094077818 +TR2278|c0_g1_i1 wt_37 wt_GSNO -0.0407242590322052 15.424279874284 0.616230913043451 0.69092556916993 +TR1492|c0_g1_i2 wt_37 wt_GSNO 0.0323916193661019 17.1363857315734 0.39613877470297 0.472810795613223 |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf |
| b |
| Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_GSNO.voom.DE_results.MA_n_Volcano.pdf has changed |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Mon Jan 22 11:28:19 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results Thu Jun 14 03:12:12 2018 -0400 |
| b |
| b'@@ -1,39 +1,39 @@\n sampleA\tsampleB\tbaseMeanA\tbaseMeanB\tbaseMean\tlog2FoldChange\tlfcSE\tstat\tpvalue\tpadj\n-TR4277|c0_g1_i1\twt_37\twt_ph8\t4705.34614971641\t162.902721493704\t2434.12443560506\t4.84804012036106\t0.130783542648097\t37.0691909868646\t8.81406568413535e-301\t3.34934495997143e-299\n-TR131|c0_g1_i1\twt_37\twt_ph8\t32.0461070493257\t1436.30905989883\t734.177583474076\t-5.48335951236111\t0.197548955320184\t-27.7569653733364\t1.43583336471356e-169\t2.72808339295576e-168\n-TR3091|c0_g1_i1\twt_37\twt_ph8\t20.4914097091341\t321.651020117047\t171.071214913091\t-3.97084930318667\t0.245881056057371\t-16.1494722971263\t1.14537343838751e-58\t1.45080635529084e-57\n-TR4761|c0_g1_i1\twt_37\twt_ph8\t2012.6141923276\t384.620292965437\t1198.61724264652\t2.38432084623308\t0.148099583891604\t16.0994432501458\t2.57410332221217e-58\t2.44539815610156e-57\n-TR5075|c0_g1_i1\twt_37\twt_ph8\t19.3833722195684\t136.98672801182\t78.1850501156942\t-2.80247674171473\t0.269715041166808\t-10.3905096637956\t2.73885623424733e-25\t2.08153073802797e-24\n-TR2779|c0_g1_i1\twt_37\twt_ph8\t191.51955185349\t1058.15934185376\t624.839446853626\t-2.45909834872711\t0.247058756007882\t-9.95349603658112\t2.43476309780354e-23\t1.54201662860891e-22\n-TR1891|c0_g1_i1\twt_37\twt_ph8\t131.416087212132\t376.595292171713\t254.005689691923\t-1.51504907455703\t0.163541333568612\t-9.26401320997792\t1.96889433896152e-20\t1.06882835543625e-19\n-TR1492|c0_g1_i2\twt_37\twt_ph8\t2006.11782336441\t890.823502721036\t1448.47066304272\t1.17018000582475\t0.127273970398445\t9.19418167093695\t3.77859650812701e-20\t1.79483334136033e-19\n-TR2487|c0_g1_i1\twt_37\twt_ph8\t418.818667162757\t965.862817209246\t692.340742186001\t-1.2054117169244\t0.138501088570193\t-8.70326529104133\t3.22468912161225e-18\t1.36153540690295e-17\n-TR3638|c0_g1_i1\twt_37\twt_ph8\t713.131183384274\t326.063958913919\t519.597571149096\t1.12815426477841\t0.141332330235517\t7.98228022490288\t1.43654437320665e-15\t5.45886861818526e-15\n-TR2107|c1_g1_i1\twt_37\twt_ph8\t59.5986596731862\t1.89840873462066\t30.7485342039034\t4.82151434610286\t0.613172060454942\t7.86323229164347\t3.74345886500564e-15\t1.29319488063831e-14\n-TR2122|c0_g2_i2\twt_37\twt_ph8\t146.135958637131\t360.821667264163\t253.478812950647\t-1.30371385707787\t0.169650604759161\t-7.68469914344628\t1.53356953387865e-14\t4.85630352394907e-14\n-TR1479|c0_g1_i1\twt_37\twt_ph8\t158.005105094407\t334.827472148091\t246.416288621249\t-1.0787542477693\t0.165556938369539\t-6.51591083039607\t7.22498877976404e-11\t2.1119197971618e-10\n-TR24|c0_g1_i1\twt_37\twt_ph8\t85.6614643869141\t199.923709280262\t142.792586833588\t-1.2279226670979\t0.196562275775691\t-6.24699048814003\t4.18436531652641e-10\t1.13575630020003e-09\n-TR4163|c0_g1_i1\twt_37\twt_ph8\t424.593720981574\t227.471218917767\t326.03246994967\t0.900981410818221\t0.155876696706134\t5.78009048085484\t7.46604610022994e-09\t1.89139834539158e-08\n-TR1449|c0_g1_i1\twt_37\twt_ph8\t220.782434528097\t117.26089394399\t169.021664236043\t0.914395516820343\t0.174920034977504\t5.22750591113215\t1.71811907274331e-07\t4.08053279776536e-07\n-TR2278|c0_g1_i1\twt_37\twt_ph8\t594.657329919233\t348.341653317169\t471.499491618201\t0.772496794598277\t0.157892732036131\t4.89254182023719\t9.95419556957436e-07\t2.2250554802578e-06\n-TR5055|c0_g2_i1\twt_37\twt_ph8\t28.6665933385886\t6.05959103586122\t17.3630921872249\t2.18372312866756\t0.505600668447204\t4.31906693354301\t1.5669025864333e-05\t3.30790546024808e-05\n-TR127|c1_g1_i1\twt_37\twt_ph8\t16.3791628279609\t1.58772512712498\t8.98344397754296\t3.22742307122337\t0.758365755070441\t4.25576056097574\t2.08339575851481e-05\t4.16679151702962e-05\n-TR1894|c2_g1_i1\twt_37\twt_ph8\t16.2826445742552\t1.67571344127509\t8.97917900776516\t3.18830464179373\t0.7590595028564\t4.20033558607184\t2.66519649541344e-05\t5.06387334128554e-05\n-TR2672|c0_g1_i1\twt_37\twt_ph8\t22.3129914439134\t7.89947501226409\t15.1062332280887\t1.46563545973546\t0.482353842293509\t3.0385068620302\t0.00237753690029721\t0.00429545997952877\n-TR4859|c0_g1_i1\twt_37\twt_ph8\t8.91205730249659\t1.28188505334354\t5.09697117792006\t2.65126611500267\t0.876469721997014\t3.02493748325022\t0.00248684525130613\t0.00429545997952877\n-TR1678|c0_g1_i1\twt_37\twt_ph8\t0.738899982352'..b'11\t5.78001251078543\t7.46950706226027e-09\t1.89227512243927e-08\n+TR1449|c0_g1_i1\twt_37\twt_ph8\t220.782434528097\t117.26089394399\t169.021664236043\t0.916182468982544\t0.175267159439457\t5.22734819182726\t1.71958482582468e-07\t4.0840139613336e-07\n+TR2278|c0_g1_i1\twt_37\twt_ph8\t594.657329919233\t348.341653317169\t471.499491618201\t0.77372548280461\t0.158144801146882\t4.8925129197639\t9.95565784679233e-07\t2.22538234222417e-06\n+TR5055|c0_g2_i1\twt_37\twt_ph8\t28.6665933385886\t6.05959103586122\t17.3630921872249\t2.22056293047175\t0.515653625436263\t4.30630722045843\t1.66002467176804e-05\t3.50449652928809e-05\n+TR127|c1_g1_i1\twt_37\twt_ph8\t16.3791628279609\t1.58772512712498\t8.98344397754296\t3.35782864860774\t0.805715621214412\t4.16751091848842\t3.07943766984562e-05\t6.15887533969124e-05\n+TR1894|c2_g1_i1\twt_37\twt_ph8\t16.2826445742552\t1.67571344127509\t8.97917900776516\t3.31835899440704\t0.806156235895963\t4.1162728099709\t3.85048512190331e-05\t7.31592173161629e-05\n+TR2672|c0_g1_i1\twt_37\twt_ph8\t22.3129914439134\t7.89947501226409\t15.1062332280887\t1.4879160019133\t0.490304786216723\t3.03467566244728\t0.00240794483755529\t0.00435723351557623\n+TR4084|c0_g1_i1\twt_37\twt_ph8\t113.2594381118\t173.837287636503\t143.548362874151\t-0.610546095515356\t0.203809508378262\t-2.99567032163292\t0.00273842322103228\t0.00473000374541939\n+TR4859|c0_g1_i1\twt_37\twt_ph8\t8.91205730249659\t1.28188505334354\t5.09697117792006\t2.79846628921536\t0.943303749490582\t2.96666507551426\t0.00301048704228202\t0.00497384815681378\n+TR1678|c0_g1_i1\twt_37\twt_ph8\t0.738899982352077\t7.85275634721875\t4.29582816478541\t-3.47431884008145\t1.21198503063676\t-2.8666351087324\t0.00414861034620894\t0.00656863304816415\n+TR3807|c0_g1_i1\twt_37\twt_ph8\t4.23896204531587\t0.352255997713617\t2.29560902151474\t3.60257127355045\t1.494771199452\t2.41011552461754\t0.0159474699414718\t0.0242401543110371\n+TR1859|c3_g1_i1\twt_37\twt_ph8\t0.361569353912422\t2.25550826604853\t1.30853880998047\t-2.58650633406891\t1.68391965639604\t-1.53600340980911\t0.124537544060973\t0.181135380859875\n+TR3249|c0_g1_i1\twt_37\twt_ph8\t1.36481976577862\t4.37661229401476\t2.87071602989669\t-1.67837058189371\t1.10474169040967\t-1.51924254915312\t0.12870145482149\t0.181135380859875\n+TR2090|c0_g1_i1\twt_37\twt_ph8\t0\t5.87877087384675\t2.93938543692337\t-4.93100736412614\t3.57047444665656\t-1.38105101655149\t0.167263275059569\t0.227000159009415\n+TR1982|c2_g1_i1\twt_37\twt_ph8\t7.00144976454503\t11.520013112092\t9.26073143831853\t-0.727260398375603\t0.567300823658434\t-1.28196605406919\t0.199854554547715\t0.261878381821143\n+TR1837|c2_g1_i1\twt_37\twt_ph8\t0.377330628439655\t1.67813520813222\t1.02773291828594\t-2.14007669057536\t1.85335822648042\t-1.15470212935543\t0.248212427250959\t0.314402407851215\n+TR5212|c0_g1_i1\twt_37\twt_ph8\t80.2050001877881\t94.8352723753388\t87.5201362815635\t-0.236625075567938\t0.21614403033503\t-1.09475646956875\t0.273623341840838\t0.335409257740381\n+TR3854|c0_g1_i1\twt_37\twt_ph8\t1925.26464813324\t2107.16376011081\t2016.21420412203\t-0.130625245556183\t0.13088163358419\t-0.998041069468758\t0.318259444082768\t0.377933089848287\n+TR2844|c0_g1_i1\twt_37\twt_ph8\t193.030766468894\t213.82243412349\t203.426600296192\t-0.144061748535941\t0.17173092225162\t-0.838880654963596\t0.401536284440308\t0.450271927171228\n+TR1122|c0_g1_i1\twt_37\twt_ph8\t1.69354093201913\t0.660517838352177\t1.17702938518565\t1.3946217378633\t1.66721495733336\t0.836497856337578\t0.402874882205836\t0.450271927171228\n+TR2011|c5_g1_i1\twt_37\twt_ph8\t6.84875389533898\t4.81927837273561\t5.8340161340373\t0.48395696149425\t0.739237535887472\t0.654670438120067\t0.512679962329315\t0.556623959100399\n+TR2182|c3_g2_i6\twt_37\twt_ph8\t2.76248771922916\t1.94482465855284\t2.353656188891\t0.516404389322083\t1.10366040723297\t0.467901526536393\t0.63985501178297\t0.675402512437579\n+TR3788|c0_g1_i1\twt_37\twt_ph8\t23.7579432209456\t26.0024682525169\t24.8802057367313\t-0.125340757750783\t0.352879389384874\t-0.355194328490741\t0.722444013290729\t0.741969527163451\n+TR939|c0_g1_i1\twt_37\twt_ph8\t103.002135647151\t102.820214322362\t102.911174984756\t0.000973457550309434\t0.195891269167835\t0.00496937691222674\t0.996035027203904\t0.996035027203904\n' |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -0,0 +1,7 @@ +sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR4277|c0_g1_i1 wt_37 wt_ph8 4705.34614971641 162.902721493704 2434.12443560506 4.84804012036106 0.130783542648097 37.0691909868646 8.81406568413535e-301 3.34934495997143e-299 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR4761|c0_g1_i1 wt_37 wt_ph8 2012.6141923276 384.620292965437 1198.61724264652 2.38432084623308 0.148099583891604 16.0994432501458 2.57410332221217e-58 2.44539815610156e-57 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR2107|c1_g1_i1 wt_37 wt_ph8 59.5986596731862 1.89840873462066 30.7485342039034 4.82151434610286 0.613172060454942 7.86323229164347 3.74345886500564e-15 1.29319488063831e-14 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR5055|c0_g2_i1 wt_37 wt_ph8 28.6665933385886 6.05959103586122 17.3630921872249 2.18372312866756 0.505600668447204 4.31906693354301 1.5669025864333e-05 3.30790546024808e-05 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00 +TR127|c1_g1_i1 wt_37 wt_ph8 16.3791628279609 1.58772512712498 8.98344397754296 3.22742307122337 0.758365755070441 4.25576056097574 2.08339575851481e-05 4.16679151702962e-05 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR1894|c2_g1_i1 wt_37 wt_ph8 16.2826445742552 1.67571344127509 8.97917900776516 3.18830464179373 0.7590595028564 4.20033558607184 2.66519649541344e-05 5.06387334128554e-05 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00 |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -0,0 +1,5 @@ +sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR131|c0_g1_i1 wt_37 wt_ph8 32.0461070493257 1436.30905989883 734.177583474076 -5.48335951236111 0.197548955320184 -27.7569653733364 1.43583336471356e-169 2.72808339295576e-168 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR3091|c0_g1_i1 wt_37 wt_ph8 20.4914097091341 321.651020117047 171.071214913091 -3.97084930318667 0.245881056057371 -16.1494722971263 1.14537343838751e-58 1.45080635529084e-57 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR5075|c0_g1_i1 wt_37 wt_ph8 19.3833722195684 136.98672801182 78.1850501156942 -2.80247674171473 0.269715041166808 -10.3905096637956 2.73885623424733e-25 2.08153073802797e-24 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00 +TR2779|c0_g1_i1 wt_37 wt_ph8 191.51955185349 1058.15934185376 624.839446853626 -2.45909834872711 0.247058756007882 -9.95349603658112 2.43476309780354e-23 1.54201662860891e-22 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results Mon Jan 22 11:28:19 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -1,39 +1,39 @@ -logFC logCPM PValue FDR -TR131|c0_g1_i1 5.83867709149149 16.0447742820606 3.67956255674e-64 1.3982337715612e-62 -TR3091|c0_g1_i1 4.35104356420213 13.9337836495047 7.47918124727105e-59 1.4210444369815e-57 -TR4277|c0_g1_i1 -4.51249642920563 17.4585638169146 1.30305812944242e-53 1.65054029729373e-52 -TR5075|c0_g1_i1 3.18286810352713 12.8084040893566 8.25600206225396e-24 7.84320195914126e-23 -TR2107|c1_g1_i1 -4.48477961203985 11.2510359028096 1.80754966502889e-22 1.37373774542196e-21 -TR2779|c0_g1_i1 2.75442228103487 15.7797198210508 8.23352696880425e-15 5.21456708024269e-14 -TR1891|c0_g1_i1 1.85607282303223 14.4424161372431 4.82341414399837e-12 2.61842482102769e-11 -TR4761|c0_g1_i1 -2.05815692521639 16.4916266891202 6.53530817860542e-12 3.10427138483757e-11 -TR1479|c0_g1_i1 1.43256512308186 14.3771181295432 1.13197856555697e-09 4.77946505457389e-09 -TR2122|c0_g2_i2 1.63807722824331 14.4300672231344 2.54380104198531e-09 9.66644395954419e-09 -TR24|c0_g1_i1 1.56169455062581 13.613754007054 1.01137959952142e-08 3.49385679834671e-08 -TR2487|c0_g1_i1 1.52157644373511 15.8810635663776 2.37540305111961e-07 7.52210966187877e-07 -TR4084|c0_g1_i1 0.991060679215133 13.5661427311877 4.21767858359174e-07 1.23285989366528e-06 -TR1678|c0_g1_i1 3.62458577193226 9.02581543875671 1.43837087677047e-05 3.90414952266271e-05 -TR127|c1_g1_i1 -2.90111481011278 9.73961125813442 2.21824302925283e-05 5.61954900744051e-05 -TR1894|c2_g1_i1 -2.85359093751189 9.70265145133598 3.82707393478771e-05 9.08930059512081e-05 -TR5055|c0_g2_i1 -1.8545312748531 10.5508309427169 0.000561739096452478 0.0012556520979526 -TR2090|c0_g1_i1 5.85461418677349 8.72713197001274 0.000625444406369261 0.00132038263566844 -TR4859|c0_g1_i1 -2.31469487039419 9.12085022188999 0.00236706272759891 0.00473412545519782 -TR1492|c0_g1_i2 -0.847097868783511 16.8160271449712 0.00265383515294934 0.00504228679060374 -TR3638|c0_g1_i1 -0.812580107843708 15.3469752226999 0.00403607816905259 0.00730337954399992 -TR3807|c0_g1_i1 -2.92018331334326 8.37863764275674 0.0119536481076316 0.0206472103677272 -TR1449|c0_g1_i1 -0.576747771663695 13.7363876885022 0.0130185393324759 0.0215088910710471 -TR1982|c2_g1_i1 1.11743546508384 9.86122459596308 0.024471659211255 0.0382656346855499 -TR2672|c0_g1_i1 -1.09825528852042 10.4080374441724 0.025174759661546 0.0382656346855499 -TR3249|c0_g1_i1 2.00776956676821 8.66772655901099 0.0275363688345113 0.0402454621427472 -TR5212|c0_g1_i1 0.582012857882519 12.8600915149255 0.0318599127004672 0.0448398771339909 -TR4163|c0_g1_i1 -0.585935901552979 14.6858409740027 0.0333717283041774 0.0452902026985264 -TR2844|c0_g1_i1 0.484938504762758 14.0537413817093 0.0410237194953782 0.0537552186491163 -TR1859|c3_g1_i1 2.64648031785777 8.0811923384908 0.0677782555815868 0.0858524570700099 -TR2278|c0_g1_i1 -0.462893051132405 15.2205527935145 0.0990317248813937 0.121393727273966 -TR3854|c0_g1_i1 0.45233145936844 17.3656486469949 0.115995274036176 0.13774438791796 -TR3788|c0_g1_i1 0.512277745155381 11.1125640718165 0.129462204245195 0.149077689736891 -TR939|c0_g1_i1 0.343195417039388 13.0829763503018 0.196684960972624 0.219824368145874 -TR1837|c2_g1_i1 2.21076601464763 7.9226544260522 0.248563909756302 0.269869387735413 -TR1122|c0_g1_i1 -0.860567840252952 7.98418712954456 0.72405804618472 0.764283493194982 -TR2011|c5_g1_i1 -0.075980865610854 9.27931055760989 0.901508002533997 0.925873083683564 -TR2182|c3_g2_i6 -0.147124070779728 8.45393312498213 1 1 +sampleA sampleB logFC logCPM PValue FDR +TR131|c0_g1_i1 wt_37 wt_ph8 -5.83867709149149 16.0447742820606 3.67956255674e-64 1.3982337715612e-62 +TR3091|c0_g1_i1 wt_37 wt_ph8 -4.35104356420213 13.9337836495047 7.47918124727105e-59 1.4210444369815e-57 +TR4277|c0_g1_i1 wt_37 wt_ph8 4.51249642920563 17.4585638169146 1.30305812944242e-53 1.65054029729373e-52 +TR5075|c0_g1_i1 wt_37 wt_ph8 -3.18286810352713 12.8084040893566 8.25600206225396e-24 7.84320195914126e-23 +TR2107|c1_g1_i1 wt_37 wt_ph8 4.48477961203985 11.2510359028096 1.80754966502889e-22 1.37373774542196e-21 +TR2779|c0_g1_i1 wt_37 wt_ph8 -2.75442228103487 15.7797198210508 8.23352696880425e-15 5.21456708024269e-14 +TR1891|c0_g1_i1 wt_37 wt_ph8 -1.85607282303223 14.4424161372431 4.82341414399837e-12 2.61842482102769e-11 +TR4761|c0_g1_i1 wt_37 wt_ph8 2.05815692521639 16.4916266891202 6.53530817860542e-12 3.10427138483757e-11 +TR1479|c0_g1_i1 wt_37 wt_ph8 -1.43256512308186 14.3771181295432 1.13197856555697e-09 4.77946505457389e-09 +TR2122|c0_g2_i2 wt_37 wt_ph8 -1.63807722824331 14.4300672231344 2.54380104198531e-09 9.66644395954419e-09 +TR24|c0_g1_i1 wt_37 wt_ph8 -1.56169455062581 13.613754007054 1.01137959952142e-08 3.49385679834671e-08 +TR2487|c0_g1_i1 wt_37 wt_ph8 -1.52157644373511 15.8810635663776 2.37540305111961e-07 7.52210966187877e-07 +TR4084|c0_g1_i1 wt_37 wt_ph8 -0.991060679215133 13.5661427311877 4.21767858359174e-07 1.23285989366528e-06 +TR1678|c0_g1_i1 wt_37 wt_ph8 -3.62458577193226 9.02581543875671 1.43837087677047e-05 3.90414952266271e-05 +TR127|c1_g1_i1 wt_37 wt_ph8 2.90111481011278 9.73961125813442 2.21824302925283e-05 5.61954900744051e-05 +TR1894|c2_g1_i1 wt_37 wt_ph8 2.85359093751189 9.70265145133598 3.82707393478771e-05 9.08930059512081e-05 +TR5055|c0_g2_i1 wt_37 wt_ph8 1.8545312748531 10.5508309427169 0.000561739096452478 0.0012556520979526 +TR2090|c0_g1_i1 wt_37 wt_ph8 -5.85461418677349 8.72713197001274 0.000625444406369261 0.00132038263566844 +TR4859|c0_g1_i1 wt_37 wt_ph8 2.31469487039419 9.12085022188999 0.00236706272759891 0.00473412545519782 +TR1492|c0_g1_i2 wt_37 wt_ph8 0.847097868783511 16.8160271449712 0.00265383515294934 0.00504228679060374 +TR3638|c0_g1_i1 wt_37 wt_ph8 0.812580107843708 15.3469752226999 0.00403607816905259 0.00730337954399992 +TR3807|c0_g1_i1 wt_37 wt_ph8 2.92018331334326 8.37863764275674 0.0119536481076316 0.0206472103677272 +TR1449|c0_g1_i1 wt_37 wt_ph8 0.576747771663695 13.7363876885022 0.0130185393324759 0.0215088910710471 +TR1982|c2_g1_i1 wt_37 wt_ph8 -1.11743546508384 9.86122459596308 0.024471659211255 0.0382656346855499 +TR2672|c0_g1_i1 wt_37 wt_ph8 1.09825528852042 10.4080374441724 0.025174759661546 0.0382656346855499 +TR3249|c0_g1_i1 wt_37 wt_ph8 -2.00776956676821 8.66772655901099 0.0275363688345113 0.0402454621427472 +TR5212|c0_g1_i1 wt_37 wt_ph8 -0.582012857882519 12.8600915149255 0.0318599127004672 0.0448398771339909 +TR4163|c0_g1_i1 wt_37 wt_ph8 0.585935901552979 14.6858409740027 0.0333717283041774 0.0452902026985264 +TR2844|c0_g1_i1 wt_37 wt_ph8 -0.484938504762758 14.0537413817093 0.0410237194953782 0.0537552186491163 +TR1859|c3_g1_i1 wt_37 wt_ph8 -2.64648031785777 8.0811923384908 0.0677782555815868 0.0858524570700099 +TR2278|c0_g1_i1 wt_37 wt_ph8 0.462893051132405 15.2205527935145 0.0990317248813937 0.121393727273966 +TR3854|c0_g1_i1 wt_37 wt_ph8 -0.45233145936844 17.3656486469949 0.115995274036176 0.13774438791796 +TR3788|c0_g1_i1 wt_37 wt_ph8 -0.512277745155381 11.1125640718165 0.129462204245195 0.149077689736891 +TR939|c0_g1_i1 wt_37 wt_ph8 -0.343195417039388 13.0829763503018 0.196684960972624 0.219824368145874 +TR1837|c2_g1_i1 wt_37 wt_ph8 -2.21076601464763 7.9226544260522 0.248563909756302 0.269869387735413 +TR1122|c0_g1_i1 wt_37 wt_ph8 0.860567840252952 7.98418712954456 0.72405804618472 0.764283493194982 +TR2011|c5_g1_i1 wt_37 wt_ph8 0.075980865610854 9.27931055760989 0.901508002533997 0.925873083683564 +TR2182|c3_g2_i6 wt_37 wt_ph8 0.147124070779728 8.45393312498213 1 1 |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf |
| b |
| Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.edgeR.DE_results.MA_n_Volcano.pdf has changed |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results Mon Jan 22 11:28:19 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -1,39 +1,39 @@ -logFC logCPM PValue FDR -TR131|c0_g1_i1 5.89108692370307 16.0946870940125 4.52958285205525e-36 1.721241483781e-34 -TR4277|c0_g1_i1 -4.47812345668175 17.3786096664403 1.7008141018303e-32 3.23154679347758e-31 -TR3091|c0_g1_i1 4.37454375877296 13.9751350003907 7.58044859691792e-23 9.60190155609603e-22 -TR2779|c0_g1_i1 2.89398117484377 15.8061264352363 3.97828335136821e-18 3.7793691837998e-17 -TR5075|c0_g1_i1 3.21512246000432 12.8334153580766 2.0588784190888e-14 1.56474759850749e-13 -TR2107|c1_g1_i1 -4.32040270723487 11.0762608486921 9.69490500265428e-11 6.14010650168104e-10 -TR4761|c0_g1_i1 -2.00464775189483 16.4172477083723 2.27235196662378e-10 1.23356249616719e-09 -TR1891|c0_g1_i1 1.89490003648365 14.4620196202787 1.18363400337593e-09 5.62226151603565e-09 -TR2122|c0_g2_i2 1.68823123696301 14.4430864744705 3.40183177422869e-08 1.436328971341e-07 -TR24|c0_g1_i1 1.665273448047 13.6146325155501 1.25297628243395e-07 4.76130987324901e-07 -TR2487|c0_g1_i1 1.57111929409713 15.8914511338271 3.01913153313087e-07 1.04297271144521e-06 -TR1479|c0_g1_i1 1.45195340320994 14.3929474544484 1.34694977997748e-06 4.2653409699287e-06 -TR1678|c0_g1_i1 3.32711159096413 8.62991286220581 4.44668660347576e-05 0.000129980069947753 -TR127|c1_g1_i1 -2.68488776770857 9.36026180000128 0.000136507461427459 0.00037052025244596 -TR1894|c2_g1_i1 -2.65840371977461 9.30640094015976 0.000158988679158599 0.000402771320535117 -TR2090|c0_g1_i1 3.12073361486577 8.21515298661506 0.000414922023762837 0.000985439806436737 -TR5055|c0_g2_i1 -1.75449782198233 10.3047459168783 0.000987360143376457 0.0020844269693503 -TR4084|c0_g1_i1 0.990738086664283 13.5812840323914 0.000929878324478984 0.00207855154883538 -TR4859|c0_g1_i1 -2.03844841522755 8.5557148387818 0.00574511253124233 0.0114902250624847 -TR3807|c0_g1_i1 -2.27805436961797 7.32408068149202 0.00831980659467625 0.0150548881236999 -TR1859|c3_g1_i1 2.08358066039446 6.92308482511994 0.0216139227266133 0.0357099592874481 -TR1492|c0_g1_i2 -0.80292474159496 16.7717103141256 0.00797659176853916 0.0150548881236999 -TR3638|c0_g1_i1 -0.765536214533451 15.2959378061905 0.00929698340782949 0.0160584258862509 -TR2672|c0_g1_i1 -1.15555384827173 10.1973122527932 0.0235572978271919 0.0372990548930539 -TR3249|c0_g1_i1 1.48866796495104 8.06119288435276 0.0588654345124954 0.0794847966327657 -TR1982|c2_g1_i1 1.06368641289493 9.64628067316551 0.0510418091524593 0.0745995672228252 -TR1837|c2_g1_i1 1.43890969571076 6.48444225997254 0.130037630852572 0.154419686637429 -TR5212|c0_g1_i1 0.63168831011067 12.8380836623566 0.0456316928604782 0.0693601731479268 -TR4163|c0_g1_i1 -0.545743678134199 14.6411189904126 0.0582697662607788 0.0794847966327657 -TR1449|c0_g1_i1 -0.549932747054717 13.6939664483469 0.0606594500618475 0.0794847966327657 -TR2844|c0_g1_i1 0.508967050135572 14.0451022220879 0.0750763100520493 0.0950966593992624 -TR3854|c0_g1_i1 0.504473372285636 17.3527799714624 0.0956174473541405 0.117208483853463 -TR1122|c0_g1_i1 -0.501746583160273 6.50836597017328 0.595453777887275 0.628534543325457 -TR3788|c0_g1_i1 0.524753873079964 11.0311382344715 0.215975804877357 0.234488016723988 -TR2278|c0_g1_i1 -0.424377145183038 15.1829447141358 0.145500439954072 0.167545961159234 -TR2182|c3_g2_i6 0.0429471548350905 7.57134083040984 0.956400717774849 0.956400717774849 -TR939|c0_g1_i1 0.398499350568058 13.0523653134109 0.192129988432482 0.214733516483362 -TR2011|c5_g1_i1 0.0410416962762211 8.85697121679121 0.9477445647389 0.956400717774849 +sampleA sampleB logFC logCPM PValue FDR +TR131|c0_g1_i1 wt_37 wt_ph8 -5.89108692370307 16.0946870940125 5.83734002581789e-38 2.2181892098108e-36 +TR4277|c0_g1_i1 wt_37 wt_ph8 4.47812345668175 17.3786096664403 2.84916418820701e-34 5.41341195759331e-33 +TR3091|c0_g1_i1 wt_37 wt_ph8 -4.37454375877296 13.9751350003907 3.03684158911717e-24 3.84666601288175e-23 +TR2779|c0_g1_i1 wt_37 wt_ph8 -2.89398117484377 15.8061264352363 2.71183962208552e-19 2.57624764098124e-18 +TR5075|c0_g1_i1 wt_37 wt_ph8 -3.21512246000432 12.8334153580766 2.25968184332879e-15 1.71735820092988e-14 +TR2107|c1_g1_i1 wt_37 wt_ph8 4.32040270723487 11.0762608486921 1.80270537224079e-11 1.14171340241917e-10 +TR4761|c0_g1_i1 wt_37 wt_ph8 2.00464775189483 16.4172477083723 4.47039820077749e-11 2.42678759470778e-10 +TR1891|c0_g1_i1 wt_37 wt_ph8 -1.89490003648365 14.4620196202787 2.60196088184267e-10 1.23593141887527e-09 +TR2122|c0_g2_i2 wt_37 wt_ph8 -1.68823123696301 14.4430864744705 9.44150971333403e-09 3.98641521229659e-08 +TR24|c0_g1_i1 wt_37 wt_ph8 -1.665273448047 13.6146325155501 3.81691570216026e-08 1.4504279668209e-07 +TR2487|c0_g1_i1 wt_37 wt_ph8 -1.57111929409713 15.8914511338271 9.80135417366341e-08 3.3859223509019e-07 +TR1479|c0_g1_i1 wt_37 wt_ph8 -1.45195340320994 14.3929474544484 4.87972014978913e-07 1.54524471409989e-06 +TR1678|c0_g1_i1 wt_37 wt_ph8 -3.32711159096413 8.62991286220581 2.09660385386406e-05 6.12853434206418e-05 +TR127|c1_g1_i1 wt_37 wt_ph8 2.68488776770857 9.36026180000128 7.01712501052362e-05 0.000190464821714212 +TR1894|c2_g1_i1 wt_37 wt_ph8 2.65840371977461 9.30640094015976 8.26981533784737e-05 0.0002095019885588 +TR2090|c0_g1_i1 wt_37 wt_ph8 -3.12073361486577 8.21515298661506 0.000232532921389064 0.000552265688299028 +TR5055|c0_g2_i1 wt_37 wt_ph8 1.75449782198233 10.3047459168783 0.000592147419555538 0.00125008899683947 +TR4084|c0_g1_i1 wt_37 wt_ph8 -0.990738086664283 13.5812840323914 0.000555059638311732 0.00124072154446152 +TR4859|c0_g1_i1 wt_37 wt_ph8 2.03844841522755 8.5557148387818 0.00395651243262557 0.00791302486525114 +TR3807|c0_g1_i1 wt_37 wt_ph8 2.27805436961797 7.32408068149202 0.00589866928719914 0.0106737825196937 +TR1492|c0_g1_i2 wt_37 wt_ph8 0.80292474159496 16.7717103141256 0.00563666782754467 0.0106737825196937 +TR1859|c3_g1_i1 wt_37 wt_ph8 -2.08358066039446 6.92308482511994 0.0165122223690091 0.0272810630444498 +TR3638|c0_g1_i1 wt_37 wt_ph8 0.765536214533451 15.2959378061905 0.00664915219564581 0.0114848992470246 +TR2672|c0_g1_i1 wt_37 wt_ph8 1.15555384827173 10.1973122527932 0.0181178874953213 0.0286866552009254 +TR3249|c0_g1_i1 wt_37 wt_ph8 -1.48866796495104 8.06119288435276 0.0485882100928285 0.065758173656721 +TR1982|c2_g1_i1 wt_37 wt_ph8 -1.06368641289493 9.64628067316551 0.0416733207176468 0.0609071610488684 +TR1837|c2_g1_i1 wt_37 wt_ph8 -1.43890969571076 6.48444225997254 0.11393330230991 0.135295796493019 +TR5212|c0_g1_i1 wt_37 wt_ph8 -0.63168831011067 12.8380836623566 0.0369371606978983 0.0561444842608054 +TR4163|c0_g1_i1 wt_37 wt_ph8 0.545743678134199 14.6411189904126 0.0480591953597162 0.065758173656721 +TR1449|c0_g1_i1 wt_37 wt_ph8 0.549932747054717 13.6939664483469 0.0501838693696029 0.065758173656721 +TR2844|c0_g1_i1 wt_37 wt_ph8 -0.508967050135572 14.0451022220879 0.0631262591502691 0.0799599282570075 +TR3854|c0_g1_i1 wt_37 wt_ph8 -0.504473372285636 17.3527799714624 0.0818779321593283 0.100366497485628 +TR1122|c0_g1_i1 wt_37 wt_ph8 0.501746583160273 6.50836597017328 0.579206371120405 0.611384502849316 +TR3788|c0_g1_i1 wt_37 wt_ph8 -0.524753873079964 11.0311382344715 0.196342217213272 0.213171550117267 +TR2278|c0_g1_i1 wt_37 wt_ph8 0.424377145183038 15.1829447141358 0.128541258915261 0.148017207235755 +TR2182|c3_g2_i6 wt_37 wt_ph8 -0.0429471548350905 7.57134083040984 0.954463369529891 0.954463369529891 +TR939|c0_g1_i1 wt_37 wt_ph8 -0.398499350568058 13.0523653134109 0.173205070507278 0.193582137625782 +TR2011|c5_g1_i1 wt_37 wt_ph8 -0.0410416962762211 8.85697121679121 0.94542366790428 0.954463369529891 |
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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf |
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| Binary file test-data/count/exp_diff/input.matrix.wt_37_vs_wt_ph8.voom.DE_results.MA_n_Volcano.pdf has changed |
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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Mon Jan 22 11:28:19 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results Thu Jun 14 03:12:12 2018 -0400 |
| b |
| b'@@ -1,40 +1,40 @@\n sampleA\tsampleB\tbaseMeanA\tbaseMeanB\tbaseMean\tlog2FoldChange\tlfcSE\tstat\tpvalue\tpadj\n-TR2779|c0_g1_i1\twt_GSNO\twt_ph8\t195.849684476753\t966.924129135581\t581.386906806167\t-2.26327524632747\t0.139880929176731\t-16.1800129556472\t6.97797522934818e-59\t2.3027318256849e-57\n-TR1891|c0_g1_i1\twt_GSNO\twt_ph8\t128.246229498835\t343.028289972482\t235.637259735659\t-1.40437008666625\t0.103208263182426\t-13.6071477550587\t3.63141533276091e-42\t5.99183529905551e-41\n-TR4761|c0_g1_i1\twt_GSNO\twt_ph8\t184.029205648389\t351.782300021135\t267.905752834762\t-0.934295661860181\t0.0925945355062913\t-10.0901814210915\t6.10565695161207e-24\t6.71622264677328e-23\n-TR24|c0_g1_i1\twt_GSNO\twt_ph8\t39.3724575919554\t183.288101009647\t111.330279300801\t-2.12198385961523\t0.229366226812664\t-9.25150964508988\t2.21344016014191e-20\t1.82608813211707e-19\n-TR3638|c0_g1_i1\twt_GSNO\twt_ph8\t174.266398355818\t297.555274221606\t235.910836288712\t-0.755625651268871\t0.0961172743232099\t-7.86149687024996\t3.79569918101421e-15\t2.50516145946938e-14\n-TR2122|c0_g2_i2\twt_GSNO\twt_ph8\t190.673533226329\t328.707071692642\t259.690302459485\t-0.781951344246178\t0.102125767694546\t-7.65674875105918\t1.90699193392882e-14\t1.04884556366085e-13\n-TR2278|c0_g1_i1\twt_GSNO\twt_ph8\t426.804298570637\t315.99710709695\t371.400702833793\t0.428907012124225\t0.105320470989525\t4.07239929801383\t4.65313200258197e-05\t0.000219361937264579\n-TR4084|c0_g1_i1\twt_GSNO\twt_ph8\t115.544575735664\t157.970364768418\t136.757470252041\t-0.434913653199297\t0.157209464946713\t-2.76645972522529\t0.00566685842046991\t0.0233757909844384\n-TR3788|c0_g1_i1\twt_GSNO\twt_ph8\t128.115824993653\t24.010679388938\t76.0632521912957\t1.36551096405932\t0.534260069919225\t2.55589186043003\t0.0105916029199559\t0.0388358773731717\n-TR1492|c0_g1_i2\twt_GSNO\twt_ph8\t1368.89238848897\t813.514514376559\t1091.20345143276\t0.692062260203308\t0.290167592747528\t2.38504325603812\t0.0170771132686324\t0.0563544737864868\n-TR1678|c0_g1_i1\twt_GSNO\twt_ph8\t0.695005959508731\t7.10082184137838\t3.89791390044355\t-1.19229893380239\t0.533516728634619\t-2.23479203145837\t0.0254310052417055\t0.0762930157251164\n-TR5075|c0_g1_i1\twt_GSNO\twt_ph8\t8.81552188359314\t126.23137395943\t67.5234479215117\t-1.10768013972448\t0.513345367512952\t-2.15776786900981\t0.0309458842036983\t0.0851011815601704\n-TR1479|c0_g1_i1\twt_GSNO\twt_ph8\t353.92669362375\t305.546165789569\t329.736429706659\t0.210154850632672\t0.101920088147959\t2.06195711219939\t0.0392118193266939\t0.0995376952139152\n-TR1859|c3_g1_i1\twt_GSNO\twt_ph8\t0\t2.05957798928713\t1.02978899464357\t-1.01742987508067\t0.500302018271162\t-2.03363136250477\t0.0419887772494581\t1\n-TR2844|c0_g1_i1\twt_GSNO\twt_ph8\t220.566338218013\t194.214843050373\t207.390590634193\t0.185176880395552\t0.100284765132021\t1.84651058564851\t0.0648181037840442\t0.152785530348104\n-TR2107|c1_g1_i1\twt_GSNO\twt_ph8\t7.08292121571621\t1.78415791317121\t4.43353956444371\t0.951944042839851\t0.540599552522162\t1.76090423752399\t0.0782546125949942\t0.170760316089935\n-TR4669|c0_g2_i1\twt_GSNO\twt_ph8\t165.630009730314\t0\t82.8150048651569\t0.762969565911357\t0.439826422982926\t1.73470607049221\t0.0827928805284532\t0.170760316089935\n-TR2672|c0_g1_i1\twt_GSNO\twt_ph8\t2.07518941673641\t7.44710458698621\t4.76114700186131\t-0.686459125319668\t0.52860452101472\t-1.29862514986048\t0.194072602638997\t0.376729169828641\n-TR4859|c0_g1_i1\twt_GSNO\twt_ph8\t3.10763825129944\t1.1806627783491\t2.14415051482427\t0.593225714064679\t0.537217960853533\t1.10425517628294\t0.269482460872864\t0.494051178266917\n-TR3091|c0_g1_i1\twt_GSNO\twt_ph8\t312.47018793986\t293.531643106953\t303.000915523406\t0.0878939148373507\t0.0878811164283744\t1.00014563320878\t0.317240035048796\t0.536180698490786\n-TR4163|c0_g1_i1\twt_GSNO\twt_ph8\t221.469120691076\t207.118822998308\t214.293971844692\t0.0959413488001967\t0.0974696330347526\t0.984320406397642\t0.324957999085325\t0.536180698490786\n-TR1894|c2_g1_i1\twt_GSNO\twt_ph8\t2.85762748931802\t1.47338219762144\t2.16550484346973\t0.431530486406946\t0.537372709941065\t0.803037590900872\t0.421953007665329\t0.663069012045517\n-TR3249|c0_g1_i1\twt_GSNO\twt_ph8\t2.06512931203634\t4.15451161800812\t3.10982046502223\t-0.'..b'9868\t1.84652838194517\t0.0648155222548659\t0.149885895214377\n+TR2107|c1_g1_i1\twt_GSNO\twt_ph8\t7.08292121571621\t1.78415791317121\t4.43353956444371\t1.99039306371489\t1.13345482120555\t1.75604093473959\t0.0790814192380851\t0.172118383047597\n+TR2672|c0_g1_i1\twt_GSNO\twt_ph8\t2.07518941673641\t7.44710458698621\t4.76114700186131\t-1.80710364026684\t1.37881760417113\t-1.31061834052603\t0.189986739707575\t0.390528298287793\n+TR4859|c0_g1_i1\twt_GSNO\twt_ph8\t3.10763825129944\t1.1806627783491\t2.14415051482427\t1.36600125700608\t1.2414304168313\t1.10034460126467\t0.271182006077654\t0.528091274993326\n+TR3091|c0_g1_i1\twt_GSNO\twt_ph8\t312.47018793986\t293.531643106953\t303.000915523406\t0.0884824617062972\t0.0884687505769758\t1.00015498273946\t0.317235511103454\t0.572534846407878\n+TR4163|c0_g1_i1\twt_GSNO\twt_ph8\t221.469120691076\t207.118822998308\t214.293971844692\t0.0967338751775769\t0.0982736079923787\t0.984332183927538\t0.32495221012339\t0.572534846407878\n+TR1894|c2_g1_i1\twt_GSNO\twt_ph8\t2.85762748931802\t1.47338219762144\t2.16550484346973\t0.974874448083219\t1.21963227734233\t0.799318340612911\t0.424105846774723\t0.713268924121126\n+TR3249|c0_g1_i1\twt_GSNO\twt_ph8\t2.06512931203634\t4.15451161800812\t3.10982046502223\t-1.06280923847799\t1.42172379433194\t-0.747549729923031\t0.454731796166148\t0.726065302514322\n+TR5212|c0_g1_i1\twt_GSNO\twt_ph8\t102.736339436612\t86.4452993262187\t94.5908193814151\t0.250307109752951\t0.347207101059694\t0.720915871216346\t0.470961277306587\t0.726065302514322\n+TR1122|c0_g1_i1\twt_GSNO\twt_ph8\t1.29006258579706\t0.5946183773076\t0.942340481552333\t1.01745920560278\t1.75106315862361\t0.581052259932493\t0.56120523253296\t1\n+TR2011|c5_g1_i1\twt_GSNO\twt_ph8\t7.597917075274\t4.42090354598533\t6.00941031062966\t0.776221433822186\t1.38068634268934\t0.562199689981896\t0.573979972628347\t0.849490359489954\n+TR1837|c2_g1_i1\twt_GSNO\twt_ph8\t2.16507864525674\t1.46465683073113\t1.81486773799393\t0.574055870722254\t1.31330872914193\t0.437106567545105\t0.662034064585522\t0.882648546299865\n+TR1982|c2_g1_i1\twt_GSNO\twt_ph8\t5.5352448786851\t10.687042573374\t8.11114372602957\t-0.948745824078601\t2.34310116245329\t-0.404910312572778\t0.685543437736556\t0.882648546299865\n+TR2182|c3_g2_i6\twt_GSNO\twt_ph8\t1.29006258579706\t1.76655578876639\t1.52830918728173\t-0.570835750385155\t1.46441538912588\t-0.389804528567464\t0.69668109483689\t0.882648546299865\n+TR1449|c0_g1_i1\twt_GSNO\twt_ph8\t98.9943307118646\t106.843279101242\t102.918804906553\t-0.106933839690288\t0.276431863357554\t-0.386836156988073\t0.69887750768045\t0.882648546299865\n+TR4277|c0_g1_i1\twt_GSNO\twt_ph8\t153.969096204861\t149.159426886469\t151.564261545665\t0.0465928591854992\t0.127909639606222\t0.364263861026723\t0.715660983486377\t0.882648546299865\n+TR3854|c0_g1_i1\twt_GSNO\twt_ph8\t2260.55060252051\t1927.46472630351\t2094.00766441201\t0.229965172704227\t0.793466242289153\t0.289823511635197\t0.771951259799022\t0.910963182508483\n+TR127|c1_g1_i1\twt_GSNO\twt_ph8\t1.20754470361908\t1.49113571265046\t1.34934020813477\t-0.373671738849606\t1.38864714646401\t-0.269090488394483\t0.787860049737066\t0.910963182508483\n+TR2090|c0_g1_i1\twt_GSNO\twt_ph8\t9.46045896251181\t5.6546754787973\t7.55756722065455\t0.740040477295998\t3.75055668025179\t0.197314836272869\t0.843581169905129\t0.945833432923932\n+TR3807|c0_g1_i1\twt_GSNO\twt_ph8\t0.347502979754365\t0.292870809896544\t0.320186894825454\t0.331202385322154\t1.89086385045429\t0.175159298350635\t0.86095446505486\t1\n+TR131|c0_g1_i1\twt_GSNO\twt_ph8\t1275.67603302799\t1312.2934796972\t1293.9847563626\t-0.0408368749216097\t0.405274721880973\t-0.100763439506112\t0.919738250126613\t0.956831887096638\n+TR5055|c0_g2_i1\twt_GSNO\twt_ph8\t5.17791343714095\t5.60171771495863\t5.38981557604979\t-0.113901914254779\t1.2463123048955\t-0.0913911495596841\t0.927181793948424\t0.956831887096638\n+TR939|c0_g1_i1\twt_GSNO\twt_ph8\t92.2508462008296\t94.0990807885678\t93.1749634946987\t-0.0286723936076206\t0.345661698999542\t-0.0829492931690373\t0.933891858779013\t0.956831887096638\n+TR2487|c0_g1_i1\twt_GSNO\twt_ph8\t875.181494043204\t882.631049341941\t878.906271692572\t-0.0122873741271452\t0.226999049805604\t-0.0541296280212089\t0.956831887096638\t0.956831887096638\n' |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf |
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| Binary file test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.MA_n_Volcano.pdf has changed |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -0,0 +1,1 @@ +sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -0,0 +1,3 @@ +sampleA sampleB baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR2779|c0_g1_i1 wt_GSNO wt_ph8 195.849684476753 966.924129135581 581.386906806167 -2.26327524632747 0.139880929176731 -16.1800129556472 6.97797522934818e-59 2.3027318256849e-57 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TR24|c0_g1_i1 wt_GSNO wt_ph8 39.3724575919554 183.288101009647 111.330279300801 -2.12198385961523 0.229366226812664 -9.25150964508988 2.21344016014191e-20 1.82608813211707e-19 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results --- a/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results Mon Jan 22 11:28:19 2018 -0500 +++ b/test-data/count/exp_diff/input.matrix.wt_GSNO_vs_wt_ph8.edgeR.DE_results Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -1,40 +1,40 @@ -logFC logCPM PValue FDR -TR2779|c0_g1_i1 2.23948335958727 15.9163308249372 1.20766376889896e-237 4.70988869870595e-236 -TR1492|c0_g1_i2 -0.807859120941235 16.8439348559211 2.37986391219743e-61 4.64073462878498e-60 -TR1891|c0_g1_i1 1.35697452203657 14.6311197032228 1.60645028176433e-35 2.08838536629363e-34 -TR4761|c0_g1_i1 0.880921757190946 14.8138260614735 1.59143301924913e-24 1.5516471937679e-23 -TR2122|c0_g2_i2 0.729785350305026 14.7699678361852 6.52776857951534e-13 5.09165949202196e-12 -TR3854|c0_g1_i1 -0.289859344737128 17.7786469452325 6.1302236270955e-12 3.98464535761207e-11 -TR3638|c0_g1_i1 0.702510801497461 14.6355179638282 5.62335492840333e-11 3.133012031539e-10 -TR2278|c0_g1_i1 -0.490901034745758 15.2921454021456 1.53296499052609e-09 7.47320432881468e-09 -TR24|c0_g1_i1 2.16007337608378 13.5636496776551 8.67157466173412e-09 3.75768235341812e-08 -TR5075|c0_g1_i1 3.7524485458028 12.8683202800317 5.50095216588421e-08 2.14537134469484e-07 -TR4669|c0_g2_i1 -10.4044948993067 13.1110475123695 1.35189372056785e-06 4.79307773655872e-06 -TR3788|c0_g1_i1 -2.47698512550917 13.0240883091698 1.80487840553907e-05 5.86585481800198e-05 -TR1479|c0_g1_i1 -0.272661827455658 15.1172528121102 0.000483095512098729 0.00144928653629619 -TR1678|c0_g1_i1 3.02812287247775 9.36059212330112 0.0074853976481696 0.0208521791627582 -TR2107|c1_g1_i1 -1.98032359155541 9.36544178725855 0.0305238827180189 0.0756824353198294 -TR2844|c0_g1_i1 -0.244755727600329 14.4560017424587 0.0310492042337762 0.0756824353198294 -TR1859|c3_g1_i1 4.12978123132011 8.37588761488442 0.0428877609330621 0.0983895691993777 -TR3091|c0_g1_i1 -0.148576217250104 14.9963238698071 0.0547318692708507 0.11858571675351 -TR2672|c0_g1_i1 1.64029381826409 9.53984158811941 0.100507062957769 0.206303971334369 -TR4163|c0_g1_i1 -0.156926020788278 14.5006265631178 0.113620071038851 0.22155913852576 -TR4859|c0_g1_i1 -1.3062724221166 8.73091245897321 0.181160758857669 0.3364414093071 -TR4084|c0_g1_i1 0.390578563212142 13.8603174460746 0.270419882900116 0.479380701504752 -TR1982|c2_g1_i1 0.866592651710305 10.0958159836705 0.312186869456376 0.515984430920105 -TR1894|c2_g1_i1 -0.989932992780787 8.78384403630691 0.317528880566218 0.515984430920105 -TR4277|c0_g1_i1 -0.107189584823599 14.0046148411409 0.347278576725125 0.541754579691195 -TR2487|c0_g1_i1 -0.0467513454249246 16.526653433485 0.376403968202147 0.560230359736405 -TR3249|c0_g1_i1 1.00369455926223 9.08504250192555 0.387851787509819 0.560230359736405 -TR5212|c0_g1_i1 -0.310409394484433 13.3365591825697 0.416163942507532 0.572783249883747 -TR2011|c5_g1_i1 -0.799376994792807 9.70509536731836 0.425915749913555 0.572783249883747 -TR1837|c2_g1_i1 -0.59484087321072 8.66193471010726 0.588495494688377 0.76504414309489 -TR2090|c0_g1_i1 -0.766971023107968 9.89421471118339 0.638322407555079 0.8030507707951 -TR131|c0_g1_i1 -0.0187996511046741 17.0827735361623 0.697507705031756 0.850087515507453 -TR1122|c0_g1_i1 -0.908051089281089 8.22928258978683 0.753364106379395 0.890339398448377 -TR1449|c0_g1_i1 0.0452741219590205 13.4583026590017 0.919111339143084 1 -TR939|c0_g1_i1 -0.0309689709592036 13.3146949564453 0.956245904999637 1 -TR5055|c0_g2_i1 0.0548476287872344 9.62768102188797 0.999999999999985 1 -TR2182|c3_g2_i6 0.517423422896207 8.5297276065799 1 1 -TR127|c1_g1_i1 0.299043611515333 8.4576897025083 1 1 -TR3807|c0_g1_i1 -0.266132577378544 7.94319410024963 1 1 +sampleA sampleB logFC logCPM PValue FDR +TR2779|c0_g1_i1 wt_GSNO wt_ph8 -2.23948335958727 15.9163308249372 1.20766376889896e-237 4.70988869870595e-236 +TR1492|c0_g1_i2 wt_GSNO wt_ph8 0.807859120941235 16.8439348559211 2.37986391219743e-61 4.64073462878498e-60 +TR1891|c0_g1_i1 wt_GSNO wt_ph8 -1.35697452203657 14.6311197032228 1.60645028176433e-35 2.08838536629363e-34 +TR4761|c0_g1_i1 wt_GSNO wt_ph8 -0.880921757190946 14.8138260614735 1.59143301924913e-24 1.5516471937679e-23 +TR2122|c0_g2_i2 wt_GSNO wt_ph8 -0.729785350305026 14.7699678361852 6.52776857951534e-13 5.09165949202196e-12 +TR3854|c0_g1_i1 wt_GSNO wt_ph8 0.289859344737128 17.7786469452325 6.1302236270955e-12 3.98464535761207e-11 +TR3638|c0_g1_i1 wt_GSNO wt_ph8 -0.702510801497461 14.6355179638282 5.62335492840333e-11 3.133012031539e-10 +TR2278|c0_g1_i1 wt_GSNO wt_ph8 0.490901034745758 15.2921454021456 1.53296499052609e-09 7.47320432881468e-09 +TR24|c0_g1_i1 wt_GSNO wt_ph8 -2.16007337608378 13.5636496776551 8.67157466173412e-09 3.75768235341812e-08 +TR5075|c0_g1_i1 wt_GSNO wt_ph8 -3.7524485458028 12.8683202800317 5.50095216588421e-08 2.14537134469484e-07 +TR4669|c0_g2_i1 wt_GSNO wt_ph8 10.4044948993067 13.1110475123695 1.35189372056785e-06 4.79307773655872e-06 +TR3788|c0_g1_i1 wt_GSNO wt_ph8 2.47698512550917 13.0240883091698 1.80487840553907e-05 5.86585481800198e-05 +TR1479|c0_g1_i1 wt_GSNO wt_ph8 0.272661827455658 15.1172528121102 0.000483095512098729 0.00144928653629619 +TR1678|c0_g1_i1 wt_GSNO wt_ph8 -3.02812287247775 9.36059212330112 0.0074853976481696 0.0208521791627582 +TR2107|c1_g1_i1 wt_GSNO wt_ph8 1.98032359155541 9.36544178725855 0.0305238827180189 0.0756824353198294 +TR2844|c0_g1_i1 wt_GSNO wt_ph8 0.244755727600329 14.4560017424587 0.0310492042337762 0.0756824353198294 +TR1859|c3_g1_i1 wt_GSNO wt_ph8 -4.12978123132011 8.37588761488442 0.0428877609330621 0.0983895691993777 +TR3091|c0_g1_i1 wt_GSNO wt_ph8 0.148576217250104 14.9963238698071 0.0547318692708507 0.11858571675351 +TR2672|c0_g1_i1 wt_GSNO wt_ph8 -1.64029381826409 9.53984158811941 0.100507062957769 0.206303971334369 +TR4163|c0_g1_i1 wt_GSNO wt_ph8 0.156926020788278 14.5006265631178 0.113620071038851 0.22155913852576 +TR4859|c0_g1_i1 wt_GSNO wt_ph8 1.3062724221166 8.73091245897321 0.181160758857669 0.3364414093071 +TR4084|c0_g1_i1 wt_GSNO wt_ph8 -0.390578563212142 13.8603174460746 0.270419882900116 0.479380701504752 +TR1982|c2_g1_i1 wt_GSNO wt_ph8 -0.866592651710305 10.0958159836705 0.312186869456376 0.515984430920105 +TR1894|c2_g1_i1 wt_GSNO wt_ph8 0.989932992780787 8.78384403630691 0.317528880566218 0.515984430920105 +TR4277|c0_g1_i1 wt_GSNO wt_ph8 0.107189584823599 14.0046148411409 0.347278576725125 0.541754579691195 +TR2487|c0_g1_i1 wt_GSNO wt_ph8 0.0467513454249246 16.526653433485 0.376403968202147 0.560230359736405 +TR3249|c0_g1_i1 wt_GSNO wt_ph8 -1.00369455926223 9.08504250192555 0.387851787509819 0.560230359736405 +TR5212|c0_g1_i1 wt_GSNO wt_ph8 0.310409394484433 13.3365591825697 0.416163942507532 0.572783249883747 +TR2011|c5_g1_i1 wt_GSNO wt_ph8 0.799376994792807 9.70509536731836 0.425915749913555 0.572783249883747 +TR1837|c2_g1_i1 wt_GSNO wt_ph8 0.59484087321072 8.66193471010726 0.588495494688377 0.76504414309489 +TR2090|c0_g1_i1 wt_GSNO wt_ph8 0.766971023107968 9.89421471118339 0.638322407555079 0.8030507707951 +TR131|c0_g1_i1 wt_GSNO wt_ph8 0.0187996511046741 17.0827735361623 0.697507705031756 0.850087515507453 +TR1122|c0_g1_i1 wt_GSNO wt_ph8 0.908051089281089 8.22928258978683 0.753364106379395 0.890339398448377 +TR1449|c0_g1_i1 wt_GSNO wt_ph8 -0.0452741219590205 13.4583026590017 0.919111339143084 1 +TR939|c0_g1_i1 wt_GSNO wt_ph8 0.0309689709592036 13.3146949564453 0.956245904999637 1 +TR5055|c0_g2_i1 wt_GSNO wt_ph8 -0.0548476287872344 9.62768102188797 0.999999999999985 1 +TR2182|c3_g2_i6 wt_GSNO wt_ph8 -0.517423422896207 8.5297276065799 1 1 +TR127|c1_g1_i1 wt_GSNO wt_ph8 -0.299043611515333 8.4576897025083 1 1 +TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.266132577378544 7.94319410024963 1 1 |
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| @@ -1,40 +1,40 @@ -logFC logCPM PValue FDR -TR2779|c0_g1_i1 2.23795519272237 15.9076254017254 2.92187316761645e-09 1.13953053537042e-07 -TR1492|c0_g1_i2 -0.807554446371668 16.8426446227048 5.58321346448906e-08 1.08872662557537e-06 -TR24|c0_g1_i1 2.16839334936064 13.5222768601527 3.73856822091501e-07 4.86013868718952e-06 -TR3788|c0_g1_i1 -2.47096654484901 13.0144557887788 1.245732049043e-06 9.71670998253539e-06 -TR5075|c0_g1_i1 3.68481140303272 12.7944067233298 3.44359702134355e-06 2.23833806387331e-05 -TR3854|c0_g1_i1 -0.290746293924475 17.7782076349597 5.25322144866517e-07 5.12189091244854e-06 -TR1891|c0_g1_i1 1.35768165107067 14.6117632515968 5.28666359293828e-06 2.79053243123467e-05 -TR4761|c0_g1_i1 0.878920056028248 14.8002262876656 5.72416908971214e-06 2.79053243123467e-05 -TR2122|c0_g2_i2 0.730166040402744 14.7551588447381 0.000213340170514583 0.000924474072229861 -TR3638|c0_g1_i1 0.708321413581678 14.6195575978943 0.000258928735946659 0.00100982207019197 -TR2107|c1_g1_i1 -1.90861736829884 8.90712643491077 0.00457979737107378 0.0148843414559898 -TR1678|c0_g1_i1 2.86408187112217 8.67828416118206 0.00614682516189 0.01844047548567 -TR2278|c0_g1_i1 -0.503051556783977 15.2850549214884 0.00155857674629228 0.00552586300958173 -TR1859|c3_g1_i1 1.96144637998691 6.77065030795652 0.0428269385052548 0.0982500353944082 -TR2672|c0_g1_i1 1.69730734417424 8.97832173338033 0.0866262290356731 0.160877282494822 -TR1479|c0_g1_i1 -0.277933522953326 15.1098597149167 0.0157877120065803 0.0439800548754737 -TR1982|c2_g1_i1 0.859948395691952 9.74982883974683 0.0845253825418736 0.160877282494822 -TR4859|c0_g1_i1 -1.04376243585308 7.84838377560073 0.178339170085147 0.289801151388364 -TR2011|c5_g1_i1 -0.835627288758852 9.33803398810951 0.117576176969539 0.20843049553691 -TR4084|c0_g1_i1 0.383433512314591 13.8345091917852 0.0320674039619619 0.083375250301101 -TR1894|c2_g1_i1 -0.899367664455804 7.86698528437277 0.236693956821629 0.369242572641742 -TR5212|c0_g1_i1 -0.317453614519532 13.3093804544918 0.0408068910563242 0.0982500353944082 -TR2182|c3_g2_i6 0.988859576038597 7.34392475064937 0.332144974966109 0.462630500845651 -TR3249|c0_g1_i1 1.18548803762213 8.36747688877935 0.296376188714782 0.444564283072173 -TR1837|c2_g1_i1 -0.83411458992077 7.6102620160458 0.393260306376011 0.528867308574635 -TR3807|c0_g1_i1 -0.40219136988549 5.09566487188118 0.681998347783062 0.765740423023185 -TR4669|c0_g2_i1 -6.05037553674292 13.1239272719772 0.480074268471172 0.603964402270185 -TR1122|c0_g1_i1 -0.184244267394782 6.64199260311611 0.869699168726351 0.892585988955992 -TR127|c1_g1_i1 0.354388761220407 7.15556768591471 0.687202943738756 0.765740423023185 -TR2844|c0_g1_i1 -0.251980888130202 14.4425124782726 0.0594765231313145 0.128865800117848 -TR2090|c0_g1_i1 0.862128177746631 9.64998833298881 0.646749723219784 0.764340581987017 -TR3091|c0_g1_i1 -0.148831558112849 14.9878570236746 0.0841354210369957 0.160877282494822 -TR5055|c0_g2_i1 -0.0583511298028353 9.18288041060754 0.918331019801174 0.918331019801174 -TR4163|c0_g1_i1 -0.161834057105857 14.4879250602579 0.126768900432688 0.214955961603254 -TR4277|c0_g1_i1 -0.103273026252208 13.9874746529507 0.30829078508145 0.445308911784317 -TR939|c0_g1_i1 -0.0333503331526365 13.2856573711711 0.715260879184748 0.774865952450143 -TR1449|c0_g1_i1 0.049884213852527 13.4293306544833 0.75234222467997 0.793009371959969 -TR2487|c0_g1_i1 -0.0480185034754555 16.5239765307922 0.407818984620182 0.530164680006236 -TR131|c0_g1_i1 -0.0203187870937255 17.0810493411762 0.539920494505425 0.658028102678487 +sampleA sampleB logFC logCPM PValue FDR +TR2779|c0_g1_i1 wt_GSNO wt_ph8 -2.23795519272237 15.9076254017254 2.92187316761645e-09 1.13953053537042e-07 +TR1492|c0_g1_i2 wt_GSNO wt_ph8 0.807554446371668 16.8426446227048 5.58321346448906e-08 1.08872662557537e-06 +TR24|c0_g1_i1 wt_GSNO wt_ph8 -2.16839334936064 13.5222768601527 3.73856822091501e-07 4.86013868718952e-06 +TR3788|c0_g1_i1 wt_GSNO wt_ph8 2.47096654484901 13.0144557887788 1.245732049043e-06 9.71670998253539e-06 +TR5075|c0_g1_i1 wt_GSNO wt_ph8 -3.68481140303272 12.7944067233298 3.44359702134355e-06 2.23833806387331e-05 +TR3854|c0_g1_i1 wt_GSNO wt_ph8 0.290746293924475 17.7782076349597 5.25322144866517e-07 5.12189091244854e-06 +TR1891|c0_g1_i1 wt_GSNO wt_ph8 -1.35768165107067 14.6117632515968 5.28666359293828e-06 2.79053243123467e-05 +TR4761|c0_g1_i1 wt_GSNO wt_ph8 -0.878920056028248 14.8002262876656 5.72416908971214e-06 2.79053243123467e-05 +TR2122|c0_g2_i2 wt_GSNO wt_ph8 -0.730166040402744 14.7551588447381 0.000213340170514583 0.000924474072229861 +TR3638|c0_g1_i1 wt_GSNO wt_ph8 -0.708321413581678 14.6195575978943 0.000258928735946659 0.00100982207019197 +TR2107|c1_g1_i1 wt_GSNO wt_ph8 1.90861736829884 8.90712643491077 0.00457979737107378 0.0148843414559898 +TR1678|c0_g1_i1 wt_GSNO wt_ph8 -2.86408187112217 8.67828416118206 0.00614682516189 0.01844047548567 +TR2278|c0_g1_i1 wt_GSNO wt_ph8 0.503051556783977 15.2850549214884 0.00155857674629228 0.00552586300958173 +TR1859|c3_g1_i1 wt_GSNO wt_ph8 -1.96144637998691 6.77065030795652 0.0428269385052548 0.0982500353944082 +TR2672|c0_g1_i1 wt_GSNO wt_ph8 -1.69730734417424 8.97832173338033 0.0866262290356731 0.160877282494822 +TR1479|c0_g1_i1 wt_GSNO wt_ph8 0.277933522953326 15.1098597149167 0.0157877120065803 0.0439800548754737 +TR1982|c2_g1_i1 wt_GSNO wt_ph8 -0.859948395691952 9.74982883974683 0.0845253825418736 0.160877282494822 +TR4859|c0_g1_i1 wt_GSNO wt_ph8 1.04376243585308 7.84838377560073 0.178339170085147 0.289801151388364 +TR2011|c5_g1_i1 wt_GSNO wt_ph8 0.835627288758852 9.33803398810951 0.117576176969539 0.20843049553691 +TR4084|c0_g1_i1 wt_GSNO wt_ph8 -0.383433512314591 13.8345091917852 0.0320674039619619 0.083375250301101 +TR1894|c2_g1_i1 wt_GSNO wt_ph8 0.899367664455804 7.86698528437277 0.236693956821629 0.369242572641742 +TR5212|c0_g1_i1 wt_GSNO wt_ph8 0.317453614519532 13.3093804544918 0.0408068910563242 0.0982500353944082 +TR2182|c3_g2_i6 wt_GSNO wt_ph8 -0.988859576038597 7.34392475064937 0.332144974966109 0.462630500845651 +TR3249|c0_g1_i1 wt_GSNO wt_ph8 -1.18548803762213 8.36747688877935 0.296376188714782 0.444564283072173 +TR1837|c2_g1_i1 wt_GSNO wt_ph8 0.83411458992077 7.6102620160458 0.393260306376011 0.528867308574635 +TR3807|c0_g1_i1 wt_GSNO wt_ph8 0.40219136988549 5.09566487188118 0.681998347783062 0.765740423023185 +TR4669|c0_g2_i1 wt_GSNO wt_ph8 6.05037553674292 13.1239272719772 0.480074268471172 0.603964402270185 +TR1122|c0_g1_i1 wt_GSNO wt_ph8 0.184244267394782 6.64199260311611 0.869699168726351 0.892585988955992 +TR127|c1_g1_i1 wt_GSNO wt_ph8 -0.354388761220407 7.15556768591471 0.687202943738756 0.765740423023185 +TR2844|c0_g1_i1 wt_GSNO wt_ph8 0.251980888130202 14.4425124782726 0.0594765231313145 0.128865800117848 +TR2090|c0_g1_i1 wt_GSNO wt_ph8 -0.862128177746631 9.64998833298881 0.646749723219784 0.764340581987017 +TR3091|c0_g1_i1 wt_GSNO wt_ph8 0.148831558112849 14.9878570236746 0.0841354210369957 0.160877282494822 +TR5055|c0_g2_i1 wt_GSNO wt_ph8 0.0583511298028353 9.18288041060754 0.918331019801174 0.918331019801174 +TR4163|c0_g1_i1 wt_GSNO wt_ph8 0.161834057105857 14.4879250602579 0.126768900432688 0.214955961603254 +TR4277|c0_g1_i1 wt_GSNO wt_ph8 0.103273026252208 13.9874746529507 0.30829078508145 0.445308911784317 +TR939|c0_g1_i1 wt_GSNO wt_ph8 0.0333503331526365 13.2856573711711 0.715260879184748 0.774865952450143 +TR1449|c0_g1_i1 wt_GSNO wt_ph8 -0.049884213852527 13.4293306544833 0.75234222467997 0.793009371959969 +TR2487|c0_g1_i1 wt_GSNO wt_ph8 0.0480185034754555 16.5239765307922 0.407818984620182 0.530164680006236 +TR131|c0_g1_i1 wt_GSNO wt_ph8 0.0203187870937255 17.0810493411762 0.539920494505425 0.658028102678487 |
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| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/norm/Trinity_paired_unmerged_1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm/Trinity_paired_unmerged_1.fasta Thu Jun 14 03:12:12 2018 -0400 |
| [ |
| @@ -0,0 +1,14 @@ +>TRINITY_DN2_c0_g1_i1 len=229 path=[0:0-228] +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN1_c0_g1_i1 len=380 path=[0:0-379] +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG +>TRINITY_DN3_c0_g1_i1 len=669 path=[0:0-668] +GCTGCATCAGACCAAGATGAAAGCATAGTAGAACTTGCATTTCAGACAACAGGGCACATTGTCACTCTTGTATTTGAAAAACACTTTCCGGCCACCATTGATTCTTTCCAGGATGCAGTGAAGTGTTTGTCTGAATTCACATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG +>TRINITY_DN3_c0_g2_i1 len=279 path=[0:0-278] +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN3_c0_g3_i1 len=240 path=[0:0-239] +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGAGTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN3_c0_g4_i1 len=202 path=[0:0-201] +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA +>TRINITY_DN0_c0_g1_i1 len=216 path=[0:0-215] +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/norm/Trinity_paired_unmerged_1.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/norm/Trinity_paired_unmerged_1.map Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -0,0 +1,7 @@ +TRINITY_DN2_c0_g1 TRINITY_DN2_c0_g1_i1 +TRINITY_DN1_c0_g1 TRINITY_DN1_c0_g1_i1 +TRINITY_DN3_c0_g1 TRINITY_DN3_c0_g1_i1 +TRINITY_DN3_c0_g2 TRINITY_DN3_c0_g2_i1 +TRINITY_DN3_c0_g3 TRINITY_DN3_c0_g3_i1 +TRINITY_DN3_c0_g4 TRINITY_DN3_c0_g4_i1 +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/raw/Trinity.fasta --- a/test-data/raw/Trinity.fasta Mon Jan 22 11:28:19 2018 -0500 +++ b/test-data/raw/Trinity.fasta Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -43,4 +43,3 @@ CTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCT ACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCA TATGTAGACCAACATGACTTTTCAGGAAAAGACTTT - |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/raw/Trinity_single_unmerged_1.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/Trinity_single_unmerged_1.fasta Thu Jun 14 03:12:12 2018 -0400 |
| [ |
| @@ -0,0 +1,2 @@ +>TRINITY_DN0_c0_g1_i1 len=226 path=[0:0-225] +CTTTACATCTGTACCATATACATATCCACCTGAAAACATTTTCTACATCCACTGTTATATGGAATGCTTGATAAGCTTTTCATTCTAACCATCAGAGCACAGTTCACAGTATGAATACATTTCCAGTAAATCTAACCTCCCAAAACCATGCCAGGTTTGTTATTTTTAATATATTCAACATTAAATTCTGTACATAGAATAAAATCTACATCAAGCCCCGCCACCC |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/raw/Trinity_single_unmerged_1.map --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/raw/Trinity_single_unmerged_1.map Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -0,0 +1,1 @@ +TRINITY_DN0_c0_g1 TRINITY_DN0_c0_g1_i1 |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/supertranscripts/trinity_genes.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/supertranscripts/trinity_genes.fasta Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -0,0 +1,14 @@ +>TRINITY_DN1_c0_g1 +CCAAGGTAGAAAACATCCCTGCTGACAAGACCTACCTGTGACATACTCACTCTCTTAGGGCTTTTAAAGACAAGCCATTAAAATAGATGACCTTTCACAGACTGAAACTTGAATCACTGCAAAATGAATCTAGGTTGCTGTCACTTTTTCTTTTGGGTGGCGGGGCTTGATGTAGATTTTATTCTATGTACAGAATTTAATGTTGAATATATTAAAAATAACAAACCTGGCATGGTTTTGGGAGGTTAGATTTACTGGAAATGTATTCATACTGTGAACTGTGCTCTGATGGTTAGAATGAAAAGCTTATCAAGCATTCCATATAACAGTGGATGTAGAAAATGTTTTCAGGTGGATATGTATATGGTACAGATGTAAAG +>TRINITY_DN0_c0_g1 +AAATATCACAACCACCTGAACAGGAACTTGGGATAAACAGGCAATGATGAGAGCCGATGTTTTTCTGTTGGTGTTTACATTGCTCTGCTCTGTGAAAGGATCCTGCAGCAGAGGCTTCCTACCTGAAAAATGTTTCTCTCAATTGTAGTGTGTGAGTTACTGGTAAGACGCTTACACCTATAACTCAAGGTCGGAATAGTCCCTCCAGTCCCTTTAGTAACCCAGTGGC +>TRINITY_DN2_c0_g1 +TCCAGACCATCGACAACATTGTCTTCTTCCCAGCCACAAGCAAGAAGGAGGATGCAGAGAACTTAGCTGCAGCCCAGAGAGATGCAGTAGACTTCGATGTTCGAGTTGATACTCAAGACCAAGGAATGTACCGCTTTTTAACATCACAACAACTGTTCAAGCTACTGGACTGCTTATTAGAGTCGCATAGATTTGCAAAAGCATTTAATTCCAACAATGAACAGAGGACTGCTCTGTGGAAAGCAGGCTTCAAAGGCAAGTCCAAGCCCAATCTTCTAA +>TRINITY_DN2_c1_g1 +GTCTGAATTCGCATGTAATGCAGCTTTCCCAGACACAAGTATGGAAGCAATCCGACTTATTCGCCATTGTGCAAAATATGTGTCTGATAGACCGCAGGCTTTCAAGGAGTACACAAGTGATGACATGAGCGTGGCACCTGAAGACAGGGTGTGGGTGAGAGGGTGGTTCCCGATCCTCTTTGAGTTGTCTTGTATCATCAATAGATGCAAATTAGATGTAAGAACCAGGGGCTTAACAGTAATGTTTGAAATAATGAAAACATATGGCCACACTTATGAAAAACATTGGTGGCAGGACTTATTCAGAATTGTTTTCAGAATCTTTGACAACATGAAATTGCCAGAACAGCAGACAGAGAAAGCTGAATGGATGACAACAACTTGTAACCATGTCCTTTATGCAATATGTGATGTATTCACCCAGTATTTAGAAGTTCTCAGCGATGTACTTTTGGATGATATTTTTGCCCAGCTTTACTGGTGTGTACAACAAGACAATGAGCAGTTAGCACGATCTGGTACAAACTGCTTAGAAAACGTG +>TRINITY_DN2_c2_g1 +ACAAGCAGCCTGGCGTGTGGGCTGCGCATTCTCTTCCGGATGTACATGGACGAGAGCAGAGTCAGTGCCTGGGAAGAAGTCCAGCAGAGGCTTTTAAACGTCTGCAGGGAAGCGCTGAGCTACTTCCTCACTCTAACATCCGAAAGTCACCGGGAAGCCTGGACTAACTTACTGTTACTGTTCCTCACTAAAGTTCTGAAGATCAGTGACAGCAGGTTTAAAGCTCACGCATCATTCTAC +>TRINITY_DN2_c3_g1 +GGTGAAAAGTTTACTCTTGAAATCTGGGATAAAACGTGTAACTGCACCCTGGATATCTTCAAAACCACAATTCCTCACGCGCTTCTGACTTGGCGTCCCACCTCTGGCGAGGCCGAACCCCCATCTCCATCAGCTGTGAGTGAAAAGCCGTTGGATGCAATATCACAAAAATCTGTAGACATACATGATTCTATTCAACCAA +>TRINITY_DN3_c0_g1 +ATTGATTTATTTAATAAGAAACCAAAGAGAGGAATACAATACCTCCAAGAACAAGGGATGCTTGGCACCACACCCGAAGATATAGCTCAGTTCTTACATCAAGAAGAAAGATTAGACTCTACTCAGGTGGGTGAGTTCCTGGGAGATAATGATAAATTCAATAAAGAAGTCATGTATGCATATGTAGACCAACATGACTTTTCAGGAAAAGACTTT |
| b |
| diff -r 67906d99d3c0 -r 13ab393ba794 test-data/supertranscripts/trinity_genes.gtf --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/supertranscripts/trinity_genes.gtf Thu Jun 14 03:12:12 2018 -0400 |
| b |
| @@ -0,0 +1,14 @@ +TRINITY_DN1_c0_g1 Trinity_gene exon 1 380 . + . gene_id "TRINITY_DN1_c0_g1"; transcript_id "TRINITY_DN1_c0_g1_i1" + +TRINITY_DN0_c0_g1 Trinity_gene exon 1 229 . + . gene_id "TRINITY_DN0_c0_g1"; transcript_id "TRINITY_DN0_c0_g1_i1" + +TRINITY_DN2_c0_g1 Trinity_gene exon 1 279 . + . gene_id "TRINITY_DN2_c0_g1"; transcript_id "TRINITY_DN2_c0_g1_i1" + +TRINITY_DN2_c1_g1 Trinity_gene exon 1 541 . + . gene_id "TRINITY_DN2_c1_g1"; transcript_id "TRINITY_DN2_c1_g1_i1" + +TRINITY_DN2_c2_g1 Trinity_gene exon 1 240 . + . gene_id "TRINITY_DN2_c2_g1"; transcript_id "TRINITY_DN2_c2_g1_i1" + +TRINITY_DN2_c3_g1 Trinity_gene exon 1 202 . + . gene_id "TRINITY_DN2_c3_g1"; transcript_id "TRINITY_DN2_c3_g1_i1" + +TRINITY_DN3_c0_g1 Trinity_gene exon 1 216 . + . gene_id "TRINITY_DN3_c0_g1"; transcript_id "TRINITY_DN3_c0_g1_i1" + |