Mercurial > repos > iuc > isoformswitchanalyzer
changeset 5:b3f292d9f35d draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1
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--- a/IsoformSwitchAnalyzeR.R Tue May 30 08:39:23 2023 +0000 +++ b/IsoformSwitchAnalyzeR.R Fri Jun 02 10:27:16 2023 +0000 @@ -29,10 +29,23 @@ parser$add_argument("--modeSelector") parser$add_argument("--parentDir", required = FALSE, help = "Parent directory") +parser$add_argument("--condition", + action = "append", + required = FALSE, + help = "Conditions") +parser$add_argument("--sampleID", + action = "append", + required = FALSE, + help = "SampleID") +parser$add_argument("--replicate", + action = "append", + required = FALSE, + help = "Replicates") parser$add_argument("--readLength", required = FALSE, type = "integer", help = "Read length (required for stringtie)") +parser$add_argument("--pairedSamples", action = "store_true", required = FALSE, help = "Paired samples") parser$add_argument("--annotation", required = FALSE, help = "Annotation") parser$add_argument("--stringtieAnnotation", required = FALSE, help = "Stringtie annotation") parser$add_argument("--transcriptome", required = FALSE, help = "Transcriptome") @@ -344,15 +357,22 @@ readLength = args$readLength ) + if (!args$pairedSamples) { ### Make design matrix myDesign <- data.frame( - sampleID = colnames(quantificationData$abundance)[-1], - condition = gsub( - "[[:digit:]]+", - "", - colnames(quantificationData$abundance)[-1] - ) - ) + sampleID = args$sampleID, + condition = args$condition) + } else { + myDesign <- data.frame( + sampleID = args$sampleID, + condition = args$condition, + replicate = args$replicate) + } + + comparisons <- as.data.frame(cbind( + condition_1 = myDesign$condition[1], + condition_2 = myDesign$condition[length(myDesign$condition)] + )) if (args$toolSource == "stringtie") { if (!is.null(args$stringtieAnnotation)) { @@ -365,6 +385,7 @@ isoformNtFasta = args$transcriptome, addAnnotatedORFs = FALSE, showProgress = TRUE, + comparisonsToMake = comparisons, fixStringTieAnnotationProblem = args$fixStringTieAnnotationProblem ) @@ -383,6 +404,7 @@ isoformNtFasta = args$transcriptome, isoformExonAnnoation = args$annotation, showProgress = TRUE, + comparisonsToMake = comparisons, fixStringTieAnnotationProblem = args$fixStringTieAnnotationProblem ) } @@ -395,7 +417,8 @@ removeNonConvensionalChr = args$removeNonConvensionalChr, isoformExonAnnoation = args$annotation, isoformNtFasta = args$transcriptome, - showProgress = TRUE + showProgress = TRUE, + comparisonsToMake = comparisons ) }
--- a/isoformswitchanalyzer.xml Tue May 30 08:39:23 2023 +0000 +++ b/isoformswitchanalyzer.xml Fri Jun 02 10:27:16 2023 +0000 @@ -20,6 +20,9 @@ description="An undefined error occurred, please check your input carefully and contact your administrator." /> </stdio> <command><![CDATA[ + #set $conditions = list() + #set $sampleIDs = list() + #set $replicates = list() #if $functionMode.selector == 'data_import' #if $functionMode.transcriptome.is_of_type("fasta.gz"): ln -s '${functionMode.transcriptome}' './transcriptome.fasta.gz' && @@ -51,21 +54,35 @@ #set $stringtie_annotation = './stringtie_annotation.gtf' #end if #end if + #else if $functionMode.tool_source.selector == 'salmon' + #set $filename = 'quant.sf' #else - #set $filename = 'quant.sf' + #set $filename = 'abundance.tsv' #end if - #for $index in range(len($functionMode.first_factor.trans_counts)): - mkdir './input_files/${functionMode.first_factor.factorLevel}${index}/' && - ln -s $functionMode.first_factor.trans_counts[$index] './input_files/${functionMode.first_factor.factorLevel}${index}/${filename}' && + #for $index in range(len($functionMode.tool_source.first_factor.trans_counts)): + $conditions.append($functionMode.tool_source.first_factor.factorLevel) + $sampleIDs.append(str($functionMode.tool_source.first_factor.factorLevel) + str($index)) + $replicates.append($index) + mkdir './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/' && + ln -s $functionMode.tool_source.first_factor.trans_counts[$index] './input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/${filename}' && #end for - #for $index in range(len($functionMode.second_factor.trans_counts)): - mkdir './input_files/${functionMode.second_factor.factorLevel}${index}/' && - ln -s $functionMode.second_factor.trans_counts[$index] './input_files/${functionMode.second_factor.factorLevel}${index}/${filename}' && + #for $index in range(len($functionMode.tool_source.second_factor.trans_counts)): + $conditions.append($functionMode.tool_source.second_factor.factorLevel) + $sampleIDs.append(str($functionMode.tool_source.second_factor.factorLevel) + str($index)) + $replicates.append($index) + mkdir './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/' && + ln -s $functionMode.tool_source.second_factor.trans_counts[$index] './input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/${filename}' && #end for Rscript '${__tool_directory__}/IsoformSwitchAnalyzeR.R' + #for $i, $condition in enumerate($conditions) + --condition $condition + --sampleID $sampleIDs[$i] + --replicate $replicates[$i] + #end for + $functionMode.pairedSamples --modeSelector $functionMode.selector --parentDir './input_files' --annotation $annotation @@ -207,31 +224,20 @@ <option value="second_step">Analysis part two: Plot all isoform switches and their annotation</option> </param> <when value="data_import"> - <section name="first_factor" title="1: Factor level" expanded="true"> - <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor' or 'treated'" - help="Only letters, numbers and underscores will be retained in this field"> - <sanitizer> - <valid initial="string.letters,string.digits"><add value="_" /></valid> - </sanitizer> - </param> - <param name="trans_counts" type="data" format="tabular" multiple="true" label="Transcript-level expression measurements"/> - </section> - <section name="second_factor" title="2: Factor level" expanded="true"> - <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be 'tumor' or 'treated'" - help="Only letters, numbers and underscores will be retained in this field"> - <sanitizer> - <valid initial="string.letters,string.digits"><add value="_" /></valid> - </sanitizer> - </param> - <param name="trans_counts" type="data" format="tabular" multiple="true" label="Transcript-level expression measurements"/> - </section> <conditional name="tool_source"> <param name="selector" type="select" label="Quantification data source" help="IsoformSwitchAnalyzeR has different functions for importing data from different sources."> <option value="stringtie">StringTie</option> - <option value="salmon">Salmon/Kallisto</option> + <option value="salmon">Salmon</option> + <option value="kallisto">Kallisto</option> </param> - <when value="salmon"/> + <when value="salmon"> + <expand macro="macro_inputs"/> + </when> + <when value="kallisto"> + <expand macro="macro_inputs"/> + </when> <when value="stringtie"> + <expand macro="macro_inputs"/> <param name="averageSize" type="integer" min="0" value="150" label="Average read length" help="Must be the number of base pairs sequenced. e.g. if the data quantified is 75 bp paired ends the the user should supply readLength=75" /> <param argument="fixStringTieAnnotationProblem" type="boolean" truevalue="--fixStringTieAnnotationProblem" falsevalue="" checked="true" @@ -256,13 +262,14 @@ help="Please note this different from a fasta file with the sequences of the entire genome." /> <param argument="removeNonConvensionalChr" type="boolean" truevalue="--removeNonConvensionalChr" falsevalue="" checked="false" label="Remove non-conventional chromosomes" help="These regions are typically used to annotate regions that cannot be associated to a specific region." /> + <param argument="pairedSamples" type="boolean" truevalue="--pairedSamples" falsevalue="" checked="false" label="Paired samples between factors" help="Samples + from different factors belong to the same individual (e.g. samples from same patient from health and cancerous tissues or different parts from the same plant)" /> <param name="countFiles" type="select" label="Generate count matrix files" help="If IsoformSwitchAnalyzeR is used for fixing Stringtie annotation problem, it can generate count files for analyzing differential expression with DESeq2 (when selecting collection) or CEMiTool (when secting the expression matrix format)."> <option value="disabled">Disabled</option> <option value="collection">Collection of count files</option> <option value="matrix">Expression matrix</option> </param> - </when> <!--WRAPPER FIRST STEP SECTION--> @@ -595,23 +602,23 @@ </data> </outputs> <tests> - <!-- Test 01: Data import mode--> + <!-- Test 01: Data import mode--> <test expect_num_outputs="1"> <conditional name="functionMode"> <param name="selector" value="data_import"/> <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/> <param name="transcriptome" value="transcriptome.fasta.gz"/> <param name="countFiles" value="disabled"/> - <section name="first_factor"> - <param name="factorLevel" value="health"/> - <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/> - </section> - <section name="second_factor"> - <param name="factorLevel" value="cancer"/> - <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/> - </section> <conditional name="tool_source"> <param name="selector" value="salmon"/> + <section name="first_factor"> + <param name="factorLevel" value="health"/> + <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/> + </section> + <section name="second_factor"> + <param name="factorLevel" value="cancer"/> + <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/> + </section> </conditional> </conditional> <output name="switchList" file="test01.RData" ftype="rdata" compare="sim_size" delta="100"/> @@ -623,16 +630,16 @@ <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/> <param name="transcriptome" value="transcriptome.fasta.gz"/> <param name="countFiles" value="matrix"/> - <section name="first_factor"> - <param name="factorLevel" value="health"/> - <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/> - </section> - <section name="second_factor"> - <param name="factorLevel" value="cancer"/> - <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/> - </section> <conditional name="tool_source"> <param name="selector" value="salmon"/> + <section name="first_factor"> + <param name="factorLevel" value="health"/> + <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/> + </section> + <section name="second_factor"> + <param name="factorLevel" value="cancer"/> + <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/> + </section> </conditional> </conditional> <output name="switchList" ftype="rdata"> @@ -650,16 +657,16 @@ <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/> <param name="transcriptome" value="transcriptome.fasta.gz"/> <param name="countFiles" value="collection"/> - <section name="first_factor"> - <param name="factorLevel" value="health"/> - <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/> - </section> - <section name="second_factor"> - <param name="factorLevel" value="cancer"/> - <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/> - </section> <conditional name="tool_source"> <param name="selector" value="salmon"/> + <section name="first_factor"> + <param name="factorLevel" value="health"/> + <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/> + </section> + <section name="second_factor"> + <param name="factorLevel" value="cancer"/> + <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/> + </section> </conditional> </conditional> <output name="switchList" ftype="rdata"> @@ -668,10 +675,11 @@ </assert_contents> </output> <output_collection name="collection_counts_factor1" type="list" count="2"> - <element name="cancer0_dataset" file="test03_cancer_counts.tabular" ftype="tabular" lines_diff="6"/> + <element name="health0_dataset" file="test03_health_counts.tabular" ftype="tabular" lines_diff="6"/> + </output_collection> <output_collection name="collection_counts_factor2" type="list" count="2"> - <element name="health0_dataset" file="test03_health_counts.tabular" ftype="tabular" lines_diff="6"/> + <element name="cancer0_dataset" file="test03_cancer_counts.tabular" ftype="tabular" lines_diff="6"/> </output_collection> </test> <!-- Test 04: Extract isoform switches all outputs--> @@ -867,7 +875,7 @@ </output> <output name="isoformFeatures" ftype="tabular"> <assert_contents> - <has_size value="95185" delta="100"/> + <has_size value="94888" delta="100"/> <has_text text="gene_overall_mean"/> </assert_contents> </output> @@ -1039,7 +1047,7 @@ </output> <output name="isoformFeatures" ftype="tabular"> <assert_contents> - <has_size value="99607" delta="50"/> + <has_size value="99310" delta="50"/> <has_text text="gene_overall_mean"/> </assert_contents> </output> @@ -1061,6 +1069,54 @@ </assert_contents> </output> </test> + <!-- Test 09: Kallisto input--> + <test expect_num_outputs="1"> + <conditional name="functionMode"> + <param name="selector" value="data_import"/> + <param name="genomeAnnotation" value="annotation_kallisto.gtf.gz"/> + <param name="transcriptome" value="transcriptome_kallisto.fasta.gz"/> + <param name="countFiles" value="disabled"/> + <conditional name="tool_source"> + <param name="selector" value="kallisto"/> + <section name="first_factor"> + <param name="factorLevel" value="health"/> + <param name="trans_counts" value="kallisto_cond1_rep1.tsv,kallisto_cond1_rep2.tsv"/> + </section> + <section name="second_factor"> + <param name="factorLevel" value="cancer"/> + <param name="trans_counts" value="kallisto_cond2_rep1.tsv,kallisto_cond2_rep2.tsv"/> + </section> + </conditional> + </conditional> + <output name="switchList" file="test09.RData" ftype="rdata" compare="sim_size" delta="100"/> + </test> + <!-- Test 10: Test paired samples in the experimental design--> + <test expect_num_outputs="3"> + <conditional name="functionMode"> + <param name="selector" value="data_import"/> + <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/> + <param name="transcriptome" value="transcriptome.fasta.gz"/> + <param name="pairedSamples" value="true"/> + <param name="countFiles" value="matrix"/> + <conditional name="tool_source"> + <param name="selector" value="salmon"/> + <section name="first_factor"> + <param name="factorLevel" value="health"/> + <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/> + </section> + <section name="second_factor"> + <param name="factorLevel" value="cancer"/> + <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/> + </section> + </conditional> + </conditional> + <output name="switchList" ftype="rdata"> + <assert_contents> + <has_size value="652170" delta="300"/> + </assert_contents> + </output> + <output name="sample_annotation" file="test10_samples_annotation.tabular" ftype="tabular"/> + </test> </tests> <help><![CDATA[
--- a/macros.xml Tue May 30 08:39:23 2023 +0000 +++ b/macros.xml Fri Jun 02 10:27:16 2023 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">1.20.0</token> - <token name="@SUFFIX_VERSION@">4</token> + <token name="@SUFFIX_VERSION@">5</token> <xml name="requirements"> <requirements> <requirement type="package" version="@TOOL_VERSION@">bioconductor-isoformswitchanalyzer</requirement> @@ -65,4 +65,24 @@ <param argument="onlySwitchingGenes" type="boolean" truevalue="--onlySwitchingGenes" falsevalue="" checked="true" label="Only switching genes" help="Only analyze genes with isoform switches (as indicated by the alpha and dIFcutoff parameters)" /> </xml> + <xml name="macro_inputs" token_format="tabular"> + <section name="first_factor" title="1: Factor level" expanded="true"> + <param name="factorLevel" type="text" value="FactorLevel" label="First factor level" + help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <param name="trans_counts" type="data" format="@FORMAT@" multiple="true" label="Transcript-level expression measurements"/> + </section> + <section name="second_factor" title="2: Factor level" expanded="true"> + <param name="factorLevel" type="text" value="FactorLevel" label="Second factor level" + help="Only letters, numbers and underscores will be retained in this field"> + <sanitizer> + <valid initial="string.letters,string.digits"><add value="_" /></valid> + </sanitizer> + </param> + <param name="trans_counts" type="data" format="@FORMAT@" multiple="true" label="Transcript-level expression measurements"/> + </section> + </xml> </macros> \ No newline at end of file
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_cond1_rep1.tsv Fri Jun 02 10:27:16 2023 +0000 @@ -0,0 +1,77 @@ +target_id length eff_length est_counts tpm +ENST00000506872.1 718 446.04 0 0 +ENST00000637938.2 12597 12324.1 0 0 +ENST00000283426.11 11515 11242.1 0 0 +ENST00000502646.1 1360 1087.11 0 0 +ENST00000362670.1 111 112 0 0 +ENST00000504041.1 9548 9275.11 0 0 +ENST00000328278.4 2577 2304.11 0 0 +ENST00000563761.1 564 294.612 1 1010.49 +ENST00000296824.4 9283 9010.11 324 10705.2 +ENST00000441693.2 637 365.802 0 0 +ENST00000565521.1 2881 2608.11 33 3766.77 +ENST00000651543.1 3684 3411.11 46.2982 4040.64 +ENST00000504309.5 2467 2194.11 56.8251 7710.15 +ENST00000502379.5 679 407.04 4.06138 2970.42 +ENST00000505555.5 2230 1957.11 220.948 33609 +ENST00000510361.5 2551 2278.11 0 0 +ENST00000264932.11 2693 2420.11 2233.99 274807 +ENST00000509632.5 583 313.035 2.87643 2735.54 +ENST00000504824.5 2207 1934.11 9.04017 1391.48 +ENST00000509420.5 631 359.802 1.34479 1112.69 +ENST00000514027.5 2612 2339.11 6.47819 824.489 +ENST00000514233.1 574 304.035 0 0 +ENST00000512962.5 1018 745.113 0.000209433 0.0836769 +ENST00000515752.5 2243 1970.11 7.96681 1203.86 +ENST00000511810.5 3404 3131.11 7.26322 690.577 +ENST00000515815.5 1104 831.113 0 0 +ENST00000509082.1 834 561.113 0 0 +ENST00000503674.5 2829 2556.11 16.9933 1979.15 +ENST00000507266.1 541 272.137 2.10826 2306.31 +ENST00000509564.1 1030 757.113 3.79424 1491.92 +ENST00000507522.1 1047 774.113 2.11821 814.604 +ENST00000512642.3 1085 812.113 0 0 +ENST00000614778.4 1050 777.113 0 0 +ENST00000618970.4 931 658.113 0 0 +ENST00000515587.1 855 582.113 15.0539 7698.83 +ENST00000513582.5 3505 3232.11 45.0642 4150.76 +ENST00000264933.9 1110 837.113 791.937 281636 +ENST00000505221.5 840 567.113 1.63295 857.207 +ENST00000509581.5 1156 883.113 33.4137 11263.9 +ENST00000507528.5 1093 820.113 241.334 87604.8 +ENST00000505526.1 1484 1211.11 13.6827 3363.33 +ENST00000505113.6 5820 5547.11 0 0 +ENST00000675395.1 5874 5601.11 30.7088 1632.19 +ENST00000507473.1 774 501.113 4.06073 2412.4 +ENST00000504656.1 1203 930.113 83 26565.9 +ENST00000512529.6 5310 5037.11 0.00982259 0.580532 +ENST00000511482.1 898 625.113 0 0 +ENST00000512466.1 3764 3491.11 47.5264 4052.78 +ENST00000684583.1 5667 5394.11 796.983 43985.7 +ENST00000514523.1 647 375.802 0 0 +ENST00000510400.5 674 402.04 0 0 +ENST00000316418.10 5637 5364.11 0.000139315 0.00773184 +ENST00000652417.2 2318 2045.11 5.0314 732.409 +ENST00000515206.6 2319 2046.11 15.0892 2195.43 +ENST00000504625.1 435 168.916 0 0 +ENST00000515583.1 816 543.113 0 0 +ENST00000509301.1 407 144.596 6 12353.1 +ENST00000506456.1 5531 5258.11 161.41 9138.64 +ENST00000510910.1 619 347.802 1.22557 1049.03 +ENST00000511487.1 4528 4255.11 0 0 +ENST00000507048.1 5362 5089.11 85.7287 5014.95 +ENST00000623673.1 1663 1390.11 15 3212.35 +ENST00000510441.1 613 341.802 2.21185 1926.47 +ENST00000512944.6 4120 3847.11 494.449 38262.1 +ENST00000515601.6 5748 5475.11 20.989 1141.25 +ENST00000508022.1 582 312.035 0 0 +ENST00000315013.9 4006 3733.11 191.774 15293.3 +ENST00000503889.2 5366 5093.11 0 0 +ENST00000510028.1 1242 969.113 4.09173 1256.94 +ENST00000511015.1 1091 818.113 24.6605 8973.7 +ENST00000505947.1 845 572.113 1.62295 844.511 +ENST00000510714.1 717 445.04 1.0105 675.954 +ENST00000509294.1 947 674.113 13.1583 5810.96 +ENST00000342584.3 1770 1497.11 127.567 25366.8 +ENST00000510604.1 891 618.113 2.89102 1392.4 +ENST00000502511.1 801 528.113 65.574 36964.7
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_cond1_rep2.tsv Fri Jun 02 10:27:16 2023 +0000 @@ -0,0 +1,77 @@ +target_id length eff_length est_counts tpm +ENST00000506872.1 718 444.274 0 0 +ENST00000637938.2 12597 12323.3 0 0 +ENST00000283426.11 11515 11241.3 0 0 +ENST00000502646.1 1360 1086.27 0 0 +ENST00000362670.1 111 112 0 0 +ENST00000504041.1 9548 9274.27 1 32.6632 +ENST00000328278.4 2577 2303.27 0 0 +ENST00000563761.1 564 292.246 0 0 +ENST00000296824.4 9283 9009.27 348.523 11718.7 +ENST00000441693.2 637 363.97 4.41107 3671.27 +ENST00000565521.1 2881 2607.27 36.066 4190.34 +ENST00000651543.1 3684 3410.27 53.3148 4735.84 +ENST00000504309.5 2467 2193.27 85.2248 11770.9 +ENST00000502379.5 679 405.274 1.39068 1039.48 +ENST00000505555.5 2230 1956.27 151.734 23495.8 +ENST00000510361.5 2551 2277.27 0 0 +ENST00000264932.11 2693 2419.27 2436.32 305061 +ENST00000509632.5 583 311.246 8.00272 7788.82 +ENST00000504824.5 2207 1933.27 15.291 2395.97 +ENST00000509420.5 631 357.97 0 0 +ENST00000514027.5 2612 2338.27 0 0 +ENST00000514233.1 574 302.246 0 0 +ENST00000512962.5 1018 744.274 1.59476 649.082 +ENST00000515752.5 2243 1969.27 1.12228 172.637 +ENST00000511810.5 3404 3130.27 5.06697 490.348 +ENST00000515815.5 1104 830.274 2.43286 887.634 +ENST00000509082.1 834 560.274 0 0 +ENST00000503674.5 2829 2555.27 15.7875 1871.6 +ENST00000507266.1 541 269.246 0 0 +ENST00000509564.1 1030 756.274 0 0 +ENST00000507522.1 1047 773.274 6.39579 2505.53 +ENST00000512642.3 1085 811.274 1 373.397 +ENST00000614778.4 1050 776.274 0 0 +ENST00000618970.4 931 657.274 0 0 +ENST00000515587.1 855 581.274 11.1218 5796.06 +ENST00000513582.5 3505 3231.27 39.6417 3716.35 +ENST00000264933.9 1110 836.274 773.583 280218 +ENST00000505221.5 840 566.274 11.9837 6410.65 +ENST00000509581.5 1156 882.274 35.1686 12075.1 +ENST00000507528.5 1093 819.274 185.156 68461.6 +ENST00000505526.1 1484 1210.27 13.8295 3461.47 +ENST00000505113.6 5820 5546.27 0 0 +ENST00000675395.1 5874 5600.27 29.608 1601.54 +ENST00000507473.1 774 500.274 0 0 +ENST00000504656.1 1203 929.274 63 20536.9 +ENST00000512529.6 5310 5036.27 0.00985333 0.592668 +ENST00000511482.1 898 624.274 0 0 +ENST00000512466.1 3764 3490.27 48.681 4225.11 +ENST00000684583.1 5667 5393.27 844.88 47454.9 +ENST00000514523.1 647 373.97 0 0 +ENST00000510400.5 674 400.274 0 0 +ENST00000316418.10 5637 5363.27 2.6729e-06 0.00015097 +ENST00000652417.2 2318 2044.27 0 0 +ENST00000515206.6 2319 2045.27 11.0322 1633.99 +ENST00000504625.1 435 167.336 0 0 +ENST00000515583.1 816 542.274 1 558.623 +ENST00000509301.1 407 142.562 5 10624.4 +ENST00000506456.1 5531 5257.27 68.82 3965.45 +ENST00000510910.1 619 346.614 1.19282 1042.48 +ENST00000511487.1 4528 4254.27 0 0 +ENST00000507048.1 5362 5088.27 71.6151 4263.56 +ENST00000623673.1 1663 1389.27 15 3270.7 +ENST00000510441.1 613 341.246 1.13479 1007.36 +ENST00000512944.6 4120 3846.27 494.139 38917.7 +ENST00000515601.6 5748 5474.27 25.9688 1437.02 +ENST00000508022.1 582 310.246 3.75834 3669.67 +ENST00000315013.9 4006 3732.27 178.254 14467.8 +ENST00000503889.2 5366 5092.27 0 0 +ENST00000510028.1 1242 968.274 7.07967 2214.89 +ENST00000511015.1 1091 817.274 10.0442 3722.95 +ENST00000505947.1 845 571.274 0.874441 463.686 +ENST00000510714.1 717 443.274 0 0 +ENST00000509294.1 947 673.274 25.0371 11265 +ENST00000342584.3 1770 1496.27 112.386 22753 +ENST00000510604.1 891 617.274 2.29183 1124.72 +ENST00000502511.1 801 527.274 64.032 36787.4
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_cond2_rep1.tsv Fri Jun 02 10:27:16 2023 +0000 @@ -0,0 +1,77 @@ +target_id length eff_length est_counts tpm +ENST00000506872.1 718 449.221 0 0 +ENST00000637938.2 12597 12326.9 0 0 +ENST00000283426.11 11515 11244.9 0 0 +ENST00000502646.1 1360 1089.91 0 0 +ENST00000362670.1 111 112 0 0 +ENST00000504041.1 9548 9277.91 4 127.807 +ENST00000328278.4 2577 2306.91 0 0 +ENST00000563761.1 564 296.058 0 0 +ENST00000296824.4 9283 9012.91 285.115 9377.75 +ENST00000441693.2 637 369.058 4.88497 3923.83 +ENST00000565521.1 2881 2610.91 26 2952.06 +ENST00000651543.1 3684 3413.91 61.9473 5379.15 +ENST00000504309.5 2467 2196.91 80.1376 10813.5 +ENST00000502379.5 679 411.058 1.41944 1023.66 +ENST00000505555.5 2230 1959.91 291.002 44015.3 +ENST00000510361.5 2551 2280.91 0 0 +ENST00000264932.11 2693 2422.91 1969.48 240968 +ENST00000509632.5 583 315.058 14.698 13829.6 +ENST00000504824.5 2207 1936.91 2.68364 410.732 +ENST00000509420.5 631 363.058 0 0 +ENST00000514027.5 2612 2341.91 0 0 +ENST00000514233.1 574 306.058 0 0 +ENST00000512962.5 1018 747.906 0 0 +ENST00000515752.5 2243 1972.91 0 0 +ENST00000511810.5 3404 3133.91 3.98933 377.361 +ENST00000515815.5 1104 833.906 1.14575 407.303 +ENST00000509082.1 834 565.221 0 0 +ENST00000503674.5 2829 2558.91 14.2218 1647.56 +ENST00000507266.1 541 273.635 1.05859 1146.83 +ENST00000509564.1 1030 759.906 1.16091 452.878 +ENST00000507522.1 1047 776.906 3.1164 1189.13 +ENST00000512642.3 1085 814.906 2 727.555 +ENST00000614778.4 1050 779.906 0 0 +ENST00000618970.4 931 660.906 0 0 +ENST00000515587.1 855 586.221 4.47439 2262.64 +ENST00000513582.5 3505 3234.91 36.9092 3382.33 +ENST00000264933.9 1110 839.906 778.684 274836 +ENST00000505221.5 840 571.221 1.65027 856.436 +ENST00000509581.5 1156 885.906 45.9537 15377.2 +ENST00000507528.5 1093 822.906 231.738 83481.6 +ENST00000505526.1 1484 1213.91 16.7958 4101.66 +ENST00000505113.6 5820 5549.91 0 0 +ENST00000675395.1 5874 5603.91 19.4282 1027.74 +ENST00000507473.1 774 505.221 8.20677 4815.42 +ENST00000504656.1 1203 932.906 50 15888.2 +ENST00000512529.6 5310 5039.91 69.9221 4112.78 +ENST00000511482.1 898 629.221 0.00153779 0.724499 +ENST00000512466.1 3764 3493.91 45.42 3853.71 +ENST00000684583.1 5667 5396.91 875.712 48101.6 +ENST00000514523.1 647 379.058 0 0 +ENST00000510400.5 674 406.058 0 0 +ENST00000316418.10 5637 5366.91 0.00981505 0.542141 +ENST00000652417.2 2318 2047.91 2.30569 333.76 +ENST00000515206.6 2319 2048.91 1.71773 248.529 +ENST00000504625.1 435 170.387 0 0 +ENST00000515583.1 816 547.221 0 0 +ENST00000509301.1 407 144 7 14410.5 +ENST00000506456.1 5531 5260.91 275.82 15542.1 +ENST00000510910.1 619 351.058 1.18666 1002.06 +ENST00000511487.1 4528 4257.91 0 0 +ENST00000507048.1 5362 5091.91 85.0013 4948.67 +ENST00000623673.1 1663 1392.91 26 5533.43 +ENST00000510441.1 613 345.058 1.11297 956.172 +ENST00000512944.6 4120 3849.91 84.6367 6517.06 +ENST00000515601.6 5748 5477.91 18.3009 990.376 +ENST00000508022.1 582 314.058 3.15922 2982.04 +ENST00000315013.9 4006 3735.91 546.594 43372.2 +ENST00000503889.2 5366 5095.91 5.40388e-08 3.1436e-06 +ENST00000510028.1 1242 971.906 8 2440.11 +ENST00000511015.1 1091 820.906 11.899 4296.96 +ENST00000505947.1 845 576.221 1.6427 845.11 +ENST00000510714.1 717 448.221 2.09769 1387.37 +ENST00000509294.1 947 676.906 21.6893 9498.63 +ENST00000342584.3 1770 1499.91 181.449 35862 +ENST00000510604.1 891 622.221 2.11194 1006.19 +ENST00000502511.1 801 532.221 84.3064 46958.2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/kallisto_cond2_rep2.tsv Fri Jun 02 10:27:16 2023 +0000 @@ -0,0 +1,77 @@ +target_id length eff_length est_counts tpm +ENST00000506872.1 718 442.438 0 0 +ENST00000637938.2 12597 12321.4 0 0 +ENST00000283426.11 11515 11239.4 0 0 +ENST00000502646.1 1360 1084.44 0 0 +ENST00000362670.1 111 31 0 0 +ENST00000504041.1 9548 9272.44 1 31.851 +ENST00000328278.4 2577 2301.44 0 0 +ENST00000563761.1 564 290.013 0 0 +ENST00000296824.4 9283 9007.44 249 8164.21 +ENST00000441693.2 637 363.013 1 813.569 +ENST00000565521.1 2881 2605.44 25 2833.84 +ENST00000651543.1 3684 3408.44 57.2767 4962.94 +ENST00000504309.5 2467 2191.44 23.1237 3116.34 +ENST00000502379.5 679 403.438 1.40198 1026.32 +ENST00000505555.5 2230 1954.44 307.284 46433.8 +ENST00000510361.5 2551 2275.44 6.2606 812.582 +ENST00000264932.11 2693 2417.44 2093.39 255747 +ENST00000509632.5 583 309.013 0 0 +ENST00000504824.5 2207 1931.44 0 0 +ENST00000509420.5 631 357.013 0 0 +ENST00000514027.5 2612 2336.44 0 0 +ENST00000514233.1 574 300.013 0 0 +ENST00000512962.5 1018 742.438 1.00612 400.227 +ENST00000515752.5 2243 1967.44 0.000843687 0.126647 +ENST00000511810.5 3404 3128.44 6.64806 627.601 +ENST00000515815.5 1104 828.438 0 0 +ENST00000509082.1 834 558.438 0 0 +ENST00000503674.5 2829 2553.44 21.6531 2504.45 +ENST00000507266.1 541 267.013 1.04829 1159.49 +ENST00000509564.1 1030 754.438 1.18981 465.768 +ENST00000507522.1 1047 771.438 3.18918 1220.94 +ENST00000512642.3 1085 809.438 3 1094.6 +ENST00000614778.4 1050 774.438 0 0 +ENST00000618970.4 931 655.438 0 0 +ENST00000515587.1 855 579.438 8.25647 4208.27 +ENST00000513582.5 3505 3229.44 28.1216 2571.76 +ENST00000264933.9 1110 834.438 779.961 276055 +ENST00000505221.5 840 564.438 8.15586 4267.46 +ENST00000509581.5 1156 880.438 30.9325 10376.1 +ENST00000507528.5 1093 817.438 175.222 63306.7 +ENST00000505526.1 1484 1208.44 17.7749 4344.1 +ENST00000505113.6 5820 5544.44 0 0 +ENST00000675395.1 5874 5598.44 41.5163 2190.12 +ENST00000507473.1 774 498.438 5.83051 3454.71 +ENST00000504656.1 1203 927.438 62 19743.5 +ENST00000512529.6 5310 5034.44 365.644 21449.8 +ENST00000511482.1 898 622.438 0 0 +ENST00000512466.1 3764 3488.44 29.0354 2458.18 +ENST00000684583.1 5667 5391.44 653.27 35785.3 +ENST00000514523.1 647 371.438 6.6166 5260.96 +ENST00000510400.5 674 398.438 0 0 +ENST00000316418.10 5637 5361.44 0.00973525 0.536268 +ENST00000652417.2 2318 2042.44 3.52769 510.103 +ENST00000515206.6 2319 2043.44 2.49204 360.173 +ENST00000504625.1 435 165.046 0 0 +ENST00000515583.1 816 540.438 1 546.475 +ENST00000509301.1 407 141.425 4 8353.13 +ENST00000506456.1 5531 5255.44 197.082 11075.3 +ENST00000510910.1 619 345.013 1.19925 1026.58 +ENST00000511487.1 4528 4252.44 0 0 +ENST00000507048.1 5362 5086.44 103.878 6031.53 +ENST00000623673.1 1663 1387.44 21 4470.15 +ENST00000510441.1 613 339.013 1.20287 1047.9 +ENST00000512944.6 4120 3844.44 392.51 30153.3 +ENST00000515601.6 5748 5472.44 16.0877 868.219 +ENST00000508022.1 582 308.013 6.20945 5953.89 +ENST00000315013.9 4006 3730.44 239.799 18984.7 +ENST00000503889.2 5366 5090.44 0 0 +ENST00000510028.1 1242 966.438 2.05036 626.575 +ENST00000511015.1 1091 815.438 10.2973 3729.48 +ENST00000505947.1 845 569.438 0.843712 437.587 +ENST00000510714.1 717 441.438 5.03402 3367.92 +ENST00000509294.1 947 671.438 45.3502 19947.6 +ENST00000342584.3 1770 1494.44 149.308 29506.8 +ENST00000510604.1 891 615.438 4.66116 2236.8 +ENST00000502511.1 801 525.438 113.645 63877.3
--- a/test-data/test02_counts.tabular Tue May 30 08:39:23 2023 +0000 +++ b/test-data/test02_counts.tabular Fri Jun 02 10:27:16 2023 +0000 @@ -1,355 +1,355 @@ -gene_names cancer0 cancer1 health0 health1 -AADACL3 1.33294716142329 1.60935135697703 0 0 -AADACL4 0.16565689184278 0.245447543814652 0 0 -ACAP3 66.9545762637869 99.4728681831285 1393.95324090613 1183.58827790662 -ACOT7 455.514031889104 625.643253171647 7395.10823740127 2889.86502433136 -ACTL8 2.25786678564214 2.8385206089638 6.29646468356414 9.65386190076367 -AGMAT 14.1868697001226 20.8082199337387 56.2113078807145 41.8419006164206 -AGRN 223.424831149421 331.946548429751 2144.12485688125 3783.10646304681 -AGTRAP 187.400533886563 314.973593315019 1943.78534029914 2390.03265356525 -AJAP1 8.63047529957261 13.8464275492248 2.78718070452411 0 -AKR7A2 83.7117317539189 130.289924823431 3829.83857542184 3540.61290523654 -AKR7A3 1.86761600752251 3.58107135446447 19.1848890894377 15.2519579815619 -AKR7L 1.63323529019925 1.78518588259504 12.0382831872031 11.9429611381668 -ALDH4A1 80.0692491307954 115.615849240505 588.92974612004 641.316225550933 -ALPL 598.739713486774 931.026396105693 12.5179727486086 145.603586056744 -ANGPTL7 0.111187468282468 0.164742599508691 11.7533214949055 12.3890347339164 -APITD1 27.9435627190935 40.1067500091512 802.720467188703 663.18564778364 -ARHGEF10L 80.3813346280653 125.687632167421 575.337403596391 982.752730025466 -ARHGEF16 44.2754028984311 66.8497008399258 8.93761413278206 2.14380019716824 -ARHGEF19 115.733727841445 189.932215231752 192.61472131494 216.922297485954 -ASAP3 88.368604104536 144.185270660234 977.339687032257 832.468754427446 -ATAD3A 170.332210340393 256.909438164756 2909.59238880021 1787.85567999184 -ATAD3B 115.009269719842 186.922563175749 1204.49289913673 580.698972738788 -ATAD3C 9.18645892844685 11.1689876678097 20.3511517744843 14.9657017546822 -ATP13A2 173.079288123976 259.826155166127 778.918736405516 778.83424421371 -AURKAIP1 431.089374951588 734.107961651523 9367.79479097331 6368.53564372911 -B3GALT6 34.5537089926203 48.0941285791035 1107.4652590036 1344.53791709811 -C1orf126 0.748005384270891 2.19315673139357 0 2.02937495588995 -C1orf127 0.219649529265469 1.31728558966594 0.73417113252224 0 -C1orf128 157.021218105179 205.564314627884 2055.87258399552 1840.70695418312 -C1orf130 0.270304535188066 0.445000989755816 0 0.293709236838892 -C1orf144 169.905131358614 236.936379177537 6169.84439356059 6172.79967616817 -C1orf151 81.934540083501 106.83864564802 2316.80019551674 1742.26068228731 -C1orf158 0.306319741118665 0 0 0 -C1orf159 25.4472609092091 27.0936925692478 255.003897423656 260.387760636754 -C1orf167 0.852445327466635 1.62734609336196 4.28017084616318 20.8037404760945 -C1orf170 1.12825925747856 4.0128035997215 42.2830759803238 44.6208842491559 -C1orf174 65.3123327213875 103.529715471474 1150.25066664382 1553.57631620601 -C1orf187 38.4882619397459 66.6560127067159 22.7498270005338 2.90670998197146 -C1orf200 0.140010077377323 0 0 0 -C1orf201 16.9572193953188 29.7070533850009 301.219367711266 379.623514344136 -C1orf211 14.6209036697657 26.998386277083 1.41183164282385 8.65855898698444 -C1orf213 0.518508587606857 1.88619698952573 76.5600381962453 156.763728464001 -C1orf222 0.381237303744296 0.529475492302115 0 0 -C1orf70 7.51184976845881 19.8485556995299 239.879629899723 290.034472160915 -C1orf86 225.001393970245 375.819392770559 3491.25500640192 2865.04772849532 -C1orf89 5.10917443855593 12.0376749429161 202.484599015937 212.283237977287 -C1orf93 100.534745697611 160.074553609957 1576.8889615254 1358.37868843451 -CAD 1.78359239559776 5.00082342629287 0 13.4392425305562 -CALML6 2.92860771428337 5.65982936080012 0 2.10905502038753 -CAMK2N1 14.2906082102419 26.1322888570167 8126.76185609601 16305.1258047596 -CAMTA1 200.588720737929 253.543060947236 3055.15380157953 4100.09091814611 -CAPZB 619.112320909139 991.572432852428 20316.4731362545 24041.0162369706 -CASP9 51.1870965570691 80.3510692413285 340.999216471908 304.57891159937 -CASZ1 13.6330268070182 19.042062635585 8.81866733613576 9.75816312925625 -CCDC27 0.0573867205178809 1.02033468450467 0.75773394235314 0 -CCNL2 154.506479643163 214.761548556505 1152.06879708577 1771.98482377448 -CDA 13.5485774691298 33.1982874601624 176.302023749904 350.510461917004 -CDC2L1 290.944540530384 454.207969292801 3112.41609597224 1859.4524654607 -CDC2L2 170.977132360159 246.928776496558 2067.4280282674 2282.26157605437 -CDC42 203.801007690173 285.200666437615 11564.694795414 10973.3271896535 -CELA2B 0.159866211673547 0.236811104138174 0 0 -CHD5 3.05969618009437 5.29226916471859 5.15789578430315 4.14182197419077 -CLCN6 47.6704636085561 60.4197458667943 574.076737032054 768.141520213874 -CLCNKA 2.63522828591018 8.68236787500691 0.678927560712282 0 -CLCNKB 5.15929663864343 12.8715185272746 2.32675789513133 1.78445080716628 -CLSTN1 202.476075380806 319.632083851152 5093.23897792429 6042.3182160338 -CORT 2.88722197591461 5.85418514894763 8.23077012212674 22.4610665654388 -CPSF3L 295.347158226512 486.168636281702 3790.65155484617 3288.19390910512 -CROCC 78.3541158913447 107.947902278446 165.209683502876 225.026477190003 -CTNNBIP1 77.4633730300185 121.027354039037 541.243734816617 627.657026575342 -CTRC 0 0 2.62147985845083 10.0482914559178 -Cort 1.39537707894365 1.30434109573608 5.2816642560574 0.0151412578013478 -DDI2 32.8160456278053 49.5573033486735 254.874844668067 460.575319357691 -DDOST 604.449663575025 907.98657543851 13665.5007422144 15397.9137626485 -DFFA 130.006170003179 214.639755373536 1325.04655393129 1333.60627430197 -DFFB 13.2342440141516 16.2498596905303 127.460095995143 151.574760997069 -DHRS3 87.0464324268709 116.72890181231 1019.4715318943 889.744275630948 -DNAJC11 170.344114526107 239.921012121094 2130.43084610145 1817.86818341584 -DNAJC16 19.7622965555186 25.9568339296646 344.527403240069 532.271145389955 -DVL1 134.516467764835 206.683713511138 2152.3813715147 1328.47243311826 -DVL1L1 3.31326839123532 6.78391259724545 59.8262158993051 60.6810257420504 -E2F2 10.4399946081232 18.7092348544285 97.2088092893749 35.6406449776233 -ECE1 66.4571391530656 104.799250566661 6832.6483396322 8161.51962989564 -EFHD2 53.7957629609978 89.4533777139045 2778.28294353325 2216.78314141543 -EIF4G3 88.0324265767771 124.576532306832 2013.10224443396 2895.59135213179 -ENO1 6558.87666660173 9380.2303936004 93534.3399845077 69650.8820586366 -EPHA2 77.3221844026497 91.3520663119398 1390.10455203221 695.561720381493 -EPHA8 7.41680618002836 20.4553678887687 0 0 -EPHB2 32.3112950981041 60.4351378257855 1707.12636087386 423.970018570528 -ERRFI1 61.8103776457282 74.6154646346554 2062.3064004349 3271.74502949025 -ESPN 19.6610267100338 39.4634680663325 0.451453505296478 0 -ESPNP 0.129073180931436 1.10615167601148 0 0 -EXOSC10 173.284597941512 227.633522955699 1944.55712530741 1802.75580392237 -FAM131C 2.24876951909219 6.27872574545493 58.9032768191879 46.1727202863332 -FAM132A 3.84947896587315 9.98135157830029 128.448491513426 40.4669321823919 -FAM41C 0.302278489637574 0.335905814000472 4.95347952144023 12.1516309778703 -FAM43B 5.46152884081911 6.47372226696996 2.51816321877196 0.965224952857359 -FBLIM1 111.14573835528 181.165870005859 1673.86297734934 4009.68470407822 -FBXO2 154.152795959943 320.494643776912 53.5029060412522 114.375666849763 -FBXO42 32.5697215584544 48.16155042074 573.623814141438 758.468180724696 -FBXO44 66.872920433567 104.857828313577 440.70354833884 534.287933783485 -FBXO6 3.50735527954742 4.06973374654982 375.388875588851 452.825103479876 -FHAD1 0.921397741797418 1.65506633667102 3.92992882180617 4.53163220334661 -FUCA1 17.0659023558552 22.5859660704193 173.703225947981 150.186453191324 -GABRD 4.99857114177978 7.69856396630753 0.865565912204043 0 -GALE 66.7029801712116 108.438476102006 1069.52511368286 649.188753095255 -GLTPD1 23.9392818646217 32.0156695513129 930.45330751506 848.58426405939 -GNB1 552.837447538731 914.810470156843 17713.2729458483 20611.8841648059 -GPR153 29.2904210431041 54.7774980860172 1159.24045408154 570.753283504249 -GPR157 6.9246933142833 13.2614200369664 130.905914635676 92.9695489365082 -GRHL3 3.17376836133494 4.12271726299763 0.648123796243081 0.993719066619065 -H6PD 9.73184391540445 18.8086651865309 1098.37928461226 1470.23075215424 -HES2 0.860500532694876 1.72024884210958 2.59604614402101 1.53614188010627 -HES3 187.003719783718 265.680001103292 0 0 -HES4 3.26807877298495 9.21672514534727 11.5504692743939 65.2732181635511 -HES5 0.413503700004359 0.45950633170621 0 0 -HMGCL 39.2773527873122 73.3597815846527 1688.82684523087 2363.0312070757 -HNRNPR 358.051830999552 557.471771442898 6385.71855992608 5229.07227596313 -HP1BP3 139.453393502231 177.816028016673 4186.94412612279 6078.47421848083 -HSPB7 0.394310461505414 2.0187516214347 948.162427438671 726.090182906317 -HSPG2 121.689737329714 194.674360059929 2789.41615140344 9015.0255999021 -HTR1D 13.8118225729494 29.5527048447396 0 0 -HTR6 2.35343259159145 4.61791075618961 0 0 -ICMT 166.884696441074 229.758550167118 2794.81710553285 3198.04879103838 -ID3 449.723045510507 491.937275449614 1856.58321013501 1565.24977053587 -IFFO2 11.1211442814015 15.5015656767494 254.481027389179 450.177925257366 -IGSF21 48.2382101870424 74.0827603487169 0 0 -IL22RA1 0.705781326914609 1.48216703986439 5.34585936395826 2.75585835305596 -IL28RA 26.6775412932847 37.2044611745628 0 0.262706833151213 -ISG15 119.116629191387 201.703582003596 3105.38902825296 4422.52033006602 -KCNAB2 14.472866871752 26.0071232987046 98.0568372347768 139.265892445833 -KIAA0090 75.0221900923905 106.982092747177 2619.54097689511 2814.94479083254 -KIAA0495 53.1784425108188 75.9934182768027 301.178753240637 296.492504087296 -KIAA0562 23.4536077035124 30.4155950084256 552.955561310365 757.122210924832 -KIAA1751 0.124854649064705 0.147995553518561 0 0 -KIAA2013 87.6070922762549 142.540272990766 2235.34892030079 1016.20334845621 -KIF17 15.2331384334259 40.1105728721002 62.825982814168 237.073941704818 -KIF1B 78.4463774846293 111.037884709977 958.82950446031 1462.83998698116 -KLHDC7A 29.4976583180273 34.0128833944181 0 1.70197917290678 -KLHL17 88.4149865150737 139.743229547414 402.664189240798 385.634425836106 -KLHL21 45.7081683780084 64.1115115382759 1140.79410997292 1285.06857702427 -LDLRAD2 3.59538453721335 6.68521812139144 76.1340375265393 338.51369086515 -LRRC38 0.997683514322432 1.47823110632106 0 0 -LRRC47 167.727959048214 235.517074003772 1609.60980616476 1612.38422270307 -LUZP1 54.5077436444742 74.5740215696991 793.059726494864 1259.65975718178 -LYPLA2 339.908534559412 474.507682586206 1769.12671671444 899.71679762656 -LZIC 24.5909618538249 35.5038220040877 1005.55759760837 1328.64742363139 -MAD2L2 797.802503952905 1305.4448801087 3002.54966649886 2339.60499136296 -MASP2 6.94294362970907 10.4836075684965 17.3641720890563 16.8953743526098 -MEGF6 24.9133362230742 41.5314394969293 107.890965396316 259.377741818583 -MFAP2 570.353630763356 951.524946192844 4072.22816859979 1290.37024329098 -MFN2 109.138239264186 175.569198648429 3384.37411958815 3187.33975186549 -MIB2 72.1921445934075 105.877740006373 548.104608562341 842.319837122101 -MIIP 152.156382122545 219.249266599866 749.357895700436 551.454150999317 -MMEL1 1.35218731641887 2.59812893600714 1.9457853553284 6.10731690978305 -MMP23B 7.44397573330445 13.7807209705557 42.2011921224724 16.2670454373069 -MORN1 12.1189773398316 22.5921149570219 117.104726780606 115.439591842647 -MRPL20 575.672594221529 786.216186065711 10475.7619523782 9030.95571681375 -MRTO4 115.820605846853 175.534021130212 2266.6396732955 1473.2148439687 -MST1 11.436606389674 26.2428762056621 18.1752386648597 15.1154146036243 -MSTP9 4.88016781424482 7.61152114597714 3.65209942678968 3.55005851843959 -MTHFR 24.4475063276812 29.9700789192959 582.652443982103 920.313167786806 -MTOR 124.73936895399 181.787722378907 941.518274269282 910.65217053747 -MUL1 43.3272006808776 62.561780331408 1786.27725008401 1654.45029118442 -MXRA8 17.1568275470348 30.24735314324 16870.3622806594 15899.5507870047 -MYOM3 0.310421878415021 0.976053727109405 0 0 -NADK 147.791664362847 198.074254201433 1436.260234407 1430.74198842295 -NBL1 20.0871324682544 36.2462919848782 15872.8448293203 8582.52849084122 -NBPF1 51.5703448730042 58.6048802693097 1706.92782325294 2229.62017496562 -NBPF3 7.68495419423518 9.85151423019643 363.760809561629 869.632664928996 -NECAP2 65.7636829492125 96.2138649556517 3701.02434454676 5026.27670642801 -NIPAL3 18.8632148299027 24.5281240302511 1308.81945494026 2494.67782270471 -NMNAT1 4.78702557232616 7.04611074195382 314.687302277864 420.645042396772 -NOC2L 234.728893985379 312.96361094634 3237.14842462 1785.16903474856 -NOL9 25.584267048995 30.1478510202841 399.044328237984 433.83104623246 -NPHP4 25.0160670907537 31.4174022684124 132.796837435761 130.998815020073 -NPPA 0.710192088474257 2.89406878186218 13.429851621239 27.4507568623061 -NPPB 0.705955005423599 1.74331524334027 0 0 -OTUD3 19.974820095962 26.6627640369539 85.6445817254726 116.089955401405 -PADI1 0.185516840463236 1.24182414771582 0 1.11316504418009 -PADI2 7.51899928234925 12.2918361015747 0 2.02472269658805 -PADI3 0.869450628853144 3.30460477762227 0 0.728834344112798 -PADI4 0.383826315779788 1.10110298423884 0 0 -PADI6 0 0.0707671159325972 0 0 -PANK4 41.8970367940307 68.1135465099719 638.532122052508 500.8015989744 -PARK7 1077.81774511544 1540.15324809546 24362.6961564898 24307.5268486402 -PAX7 0.21145536824581 0.0816882815741125 0 0 -PDPN 204.703088605948 309.476711243959 165.120606833283 85.5475350277717 -PER3 10.0624111654097 27.5498566921273 236.275948645371 607.667822838314 -PEX10 58.1307855336005 80.7060283478488 1151.06186639986 930.452221357871 -PEX14 73.4945032707565 107.881910331134 1371.46977439048 1094.01402382356 -PGD 890.161300907484 1280.00698110311 19121.666094945 12476.1466550127 -PHF13 77.8551548549547 121.472277853625 742.138646029597 1030.19031622626 -PIK3CD 50.9607746055481 82.4895572377791 183.485391801705 221.213373384644 -PINK1 50.0818469155858 85.5475963290434 2692.36077455866 4317.35515886264 -PLA2G2A 3.74974538819337 7.92256771625009 22.9259041929206 6.51597423568075 -PLA2G2F 0 0.122170264426813 0 0 -PLA2G5 0.201088163638666 0 277.115482877212 55.4248127286894 -PLCH2 0.193540142248261 0.544784065319548 5.22902173840885 0.616837768527375 -PLEKHG5 42.2674777253159 83.4115088410516 107.045403068473 55.8901444256815 -PLEKHM2 93.8608844360673 140.071313747926 2597.10278065526 2783.72448827927 -PLEKHN1 2.5736879406531 4.40844119860827 80.117711730481 53.72785611922 -PLOD1 109.603259722424 181.797773098397 7647.61830726864 16571.3813969054 -PNRC2 143.027070406672 152.609586312322 2011.01065422974 2090.32021814912 -PQLC2 38.0703573702872 61.4706383280928 714.709789866736 633.259418304438 -PRAMEF12 0 0.279456665890625 0 0 -PRAMEF17 0 0.106673490789535 0 0 -PRDM16 0.611027729076883 0.984067740086007 7.62453585986095 11.4951548439442 -PRDM2 18.6581906890874 28.2475997148451 394.131386140751 725.046460696322 -PRKCZ 117.712024291513 181.492407113477 53.2817718056418 161.944015592889 -PTCHD2 9.26750946108815 13.0498685446334 1.20260777463017 0 -PUSL1 94.6023146270327 149.809078960288 1102.09270198373 867.275989488539 -Pex14 13.4164623711511 17.5741837703391 583.441949667253 549.700888764663 -RAP1GAP 20.2795577553702 34.2314656737353 1.93869267311573 2.97246652674793 -RBP7 27.4187934555505 47.5241092022853 22.1452327263775 21.8273080337132 -RCAN3 17.5062860157843 22.073693461388 305.126521225719 626.138147907035 -RCC2 609.224891778857 1055.45297526727 1398.04583673645 985.098041731445 -RER1 95.2926149754708 147.338450580103 4103.2887729276 4944.55939763565 -RERE 124.283460004597 168.245837014558 1692.02943382284 3015.46946770012 -RNF186 0 0.132978736376042 0 0 -RNF207 8.17889719501219 15.6369991218838 54.0689440848903 102.812840504349 -RPL11 9264.50338715238 15259.6279877625 120354.990597382 151466.498386692 -RPL22 548.222657612127 767.825253908004 9672.8039620794 12962.5458958234 -RSC1A1 35.1225700307662 41.556494504802 304.983855853392 560.365515506551 -SAMD11 0.975266140467855 0.759252887568278 45.0300230436727 49.0319495170954 -SCNN1D 7.71336638783454 15.5462142033146 63.1275559900522 82.3917376076902 -SDF4 227.240662691068 321.830494596159 11192.2468917904 9591.92021655629 -SDHB 197.976221969527 275.147419909074 5863.32070994542 6298.70789527058 -SFRS13A 205.264479559859 266.370449636862 2681.6216041 2951.10917707711 -SH2D5 32.9533496689486 61.4520589305865 461.673162743305 234.472126490938 -SKI 92.3897739483106 127.413509412446 1927.52535349287 1842.60449966352 -SLC25A33 24.6601200693325 47.4403292762466 384.468466133855 215.085637104663 -SLC25A34 1.29825648901777 1.62759915612056 13.5765083834194 18.5813260646421 -SLC2A5 0.260483267812907 0.67541240881633 16.3041560887102 277.689332454979 -SLC2A7 0.0850275751047418 0 0 1.50881939106148 -SLC35E2 148.195682693737 196.923064964221 2067.76811117078 1857.68513708358 -SLC45A1 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0.340359169837346 0 1.80705064391604 3.84646419215375 +XLOC_000099 11.9362517122089 2.28760719149588 26.9427447128 34.947787485532 +XLOC_000129 353.587071781866 758.240294777622 18.772462633958 29.3468930311443 +XLOC_000138 202.53853151081 344.095867778729 38.8700741575041 51.7940496915431 +XLOC_000148 2.54033057482786 0.518381268897529 1.57031994775796 2.0703046333356 +XLOC_000158 0 0 1.63670091555161 4.29047267335988 +XLOC_000173 0.669622554351972 7.18675196052498 1.06214651959231 1.12407426258865 +XLOC_000174 3679.99023128108 22568.9992411476 529.705405954172 9418.1343848515 +XLOC_000179 485.640103066908 724.628699874925 53.0677442654029 80.9418864284067 +XLOC_000187 26.360772631746 15.4131952005694 1.0725849356793 1.29123388065767 +XLOC_000188 2500.18608736872 2893.71714995025 485.665022302667 730.200923926726 +XLOC_000190 0 0 0.114539036581279 0.169708372845532 +XLOC_001217 2027.34232722767 1140.52321249461 130.676612377691 209.33874703643 +XLOC_001218 9.52791266360871 0 1.11065103222938 4.57113901513204 +XLOC_001219 11.3705108476242 19.898838698614 0.28644580395248 0.462998956729158 +XLOC_001220 17.6627820045462 27.9729729298378 76.2580000478759 118.977904648644 +XLOC_001222 87.3738347178654 163.72394213182 126.034325977775 193.513860913044 +XLOC_001223 31341.9338316771 0 163547.84518143 150008.962644156 +XLOC_001225 31341.9338316771 0 163547.84518143 150008.962644156 +XLOC_001227 42.4480653881083 73.0480407662068 28.4239434935344 44.1599898071085 +XLOC_001228 37.1746781190191 53.9434758606289 2.96779776535697 2.72934466849826 +XLOC_001230 9.44420723023971 7.24002040593887 1.04098840207296 0 +XLOC_001235 0 0 0.643193954521966 1.20378544200498 +XLOC_001241 27.1926538485809 19.1088966517602 4.11476546544828 7.20519927331771 +XLOC_001249 170.271058414378 55.3105894310116 9.59909351607688 12.2964666116257 +XLOC_001255 656.756902666893 1708.04361756199 43.8864481692447 57.2375911584504 +XLOC_001261 0 0 0.90538512843992 1.62893626076707 +XLOC_001262 32.879450200818 28.7871005595427 2.57484095100331 8.57724811776433 +XLOC_001265 260.853867089462 140.036931233652 102.124501928649 178.840887319719 +XLOC_001269 10.1892351170661 27.5651269941468 0.11275216952578 0.222119105968671 +XLOC_001271 0.739963735624112 0 0 0 +XLOC_001272 3.40547383237821 18.2746745328208 0 0 +XLOC_001279 0 0 0 0.196093126802293 +XLOC_001300 61.2454109786738 99.1536701126289 29.1309548025757 32.8750060677505 +XLOC_001302 48.8092380588883 91.298890695025 26.859308595584 46.1638520055266 +XLOC_001321 2808.34205445117 1561.66669448542 304.286653369147 352.220285459156 +XLOC_001325 223.97284590171 244.287622687443 38.3463137232589 44.5659670836712 +XLOC_001335 5.3417274447352 0.450899882954414 0.500183500127258 0.594266737589076 +XLOC_001338 28354.734013617 17953.5236839171 1730.03542846583 3865.41697747869 +XLOC_001339 43.8346808379212 47.6814554489967 7.23103916627791 10.251015971773 +XLOC_001349 51.1774249153872 102.986302873693 23.8440839846515 29.2782663595089 +XLOC_001350 0.816249598627034 1.00664968225117 1.4752288850076 2.1408032514761 +XLOC_001351 1407.51704323402 2617.27714122475 21.2015565220575 33.3290832161605 +XLOC_001353 624.002928066391 695.456434884007 83.4951990071602 149.319321757687 +XLOC_001356 230.807964129475 606.651426727153 50.2094341503045 115.190039740662 +XLOC_001372 14.2153949190097 24.2174693160748 1.91582617937623 2.83861034753068 +XLOC_001379 0 5.64750205253292 0.0910349755442975 0.134883347719491 +XLOC_001388 0.70418227693387 0.539833038602494 0.0532721212125523 0.236667522431167 +XLOC_001389 475.397331693707 735.365654745429 6.75542956098647 11.622221273691 +XLOC_001394 0 0 0 0.325668438290865 +XLOC_001401 0 0 0.184850759376464 0.27372057669569 +XLOC_001404 84.3316006411086 171.862029782374 6.91245087404029 18.7625395631549 +ZBTB17 792.615674949323 724.307200079801 39.465672732615 62.8537160424089 +ZBTB40 225.002031996727 308.369466259324 36.5722648528181 24.6063437546859 +ZBTB48 285.548786027533 290.958457686854 38.6672531811893 60.54808278606 +ZNF436 381.877284921004 509.309870434116 1.88956101189413 3.81408651722365
--- a/test-data/test02_samples_annotation.tabular Tue May 30 08:39:23 2023 +0000 +++ b/test-data/test02_samples_annotation.tabular Fri Jun 02 10:27:16 2023 +0000 @@ -1,5 +1,5 @@ sampleID condition +health0 health +health1 health cancer0 cancer cancer1 cancer -health0 health -health1 health
--- a/test-data/test03_cancer_counts.tabular Tue May 30 08:39:23 2023 +0000 +++ b/test-data/test03_cancer_counts.tabular Fri Jun 02 10:27:16 2023 +0000 @@ -65,12 +65,12 @@ CLCNKA 2.63522828591018 CLCNKB 5.15929663864343 CLSTN1 202.476075380806 +Cort 1.39537707894365 CORT 2.88722197591461 CPSF3L 295.347158226512 CROCC 78.3541158913447 CTNNBIP1 77.4633730300185 CTRC 0 -Cort 1.39537707894365 DDI2 32.8160456278053 DDOST 604.449663575025 DFFA 130.006170003179 @@ -189,6 +189,7 @@ PDPN 204.703088605948 PER3 10.0624111654097 PEX10 58.1307855336005 +Pex14 13.4164623711511 PEX14 73.4945032707565 PGD 890.161300907484 PHF13 77.8551548549547 @@ -211,7 +212,6 @@ PRKCZ 117.712024291513 PTCHD2 9.26750946108815 PUSL1 94.6023146270327 -Pex14 13.4164623711511 RAP1GAP 20.2795577553702 RBP7 27.4187934555505 RCAN3 17.5062860157843
--- a/test-data/test03_health_counts.tabular Tue May 30 08:39:23 2023 +0000 +++ b/test-data/test03_health_counts.tabular Fri Jun 02 10:27:16 2023 +0000 @@ -65,12 +65,12 @@ CLCNKA 0.678927560712282 CLCNKB 2.32675789513133 CLSTN1 5093.23897792429 +Cort 5.2816642560574 CORT 8.23077012212674 CPSF3L 3790.65155484617 CROCC 165.209683502876 CTNNBIP1 541.243734816617 CTRC 2.62147985845083 -Cort 5.2816642560574 DDI2 254.874844668067 DDOST 13665.5007422144 DFFA 1325.04655393129 @@ -189,6 +189,7 @@ PDPN 165.120606833283 PER3 236.275948645371 PEX10 1151.06186639986 +Pex14 583.441949667253 PEX14 1371.46977439048 PGD 19121.666094945 PHF13 742.138646029597 @@ -211,7 +212,6 @@ PRKCZ 53.2817718056418 PTCHD2 1.20260777463017 PUSL1 1102.09270198373 -Pex14 583.441949667253 RAP1GAP 1.93869267311573 RBP7 22.1452327263775 RCAN3 305.126521225719
--- a/test-data/test04_summary.tabular Tue May 30 08:39:23 2023 +0000 +++ b/test-data/test04_summary.tabular Fri Jun 02 10:27:16 2023 +0000 @@ -1,2 +1,2 @@ Comparison nrIsoforms nrSwitches nrGenes -cancer vs health 91 70 54 +health vs cancer 91 70 54
--- a/test-data/test06_consequences_enrichment.tabular Tue May 30 08:39:23 2023 +0000 +++ b/test-data/test06_consequences_enrichment.tabular Fri Jun 02 10:27:16 2023 +0000 @@ -1,6 +1,6 @@ condition_1 condition_2 conseqPair feature propOfRelevantEvents propCiLo propCiHi propPval nUp nDown propQval Significant -cancer health NMD_status NMD insensitive (paired with NMD sensitive) 0.333333333333333 0.00840375865961264 0.905700675949754 1 1 2 1 FALSE -cancer health intron_retention Intron retention gain (paired with Intron retention loss) 0.25 0.0548606445279928 0.571858461878189 0.14599609375 3 9 0.72998046875 FALSE -cancer health isoform_length Length gain (paired with Length loss) 0.423076923076923 0.233521983127443 0.630819619076033 0.557197093963623 11 15 0.928661823272706 FALSE -cancer health tss Tss more downstream (paired with Tss more upstream) 0.575757575757576 0.392153016187885 0.745238177265304 0.486850241664797 19 14 0.928661823272706 FALSE -cancer health tts Tts more downstream (paired with Tts more upstream) 0.5 0.210944638239297 0.789055361760703 1 6 6 1 FALSE +health cancer intron_retention Intron retention gain (paired with Intron retention loss) 0.75 0.428141538121811 0.945139355472007 0.14599609375 9 3 0.72998046875 FALSE +health cancer isoform_length Length gain (paired with Length loss) 0.576923076923077 0.369180380923967 0.766478016872557 0.557197093963623 15 11 0.928661823272706 FALSE +health cancer NMD_status NMD insensitive (paired with NMD sensitive) 0.666666666666667 0.0942993240502461 0.991596241340387 1 2 1 1 FALSE +health cancer tss Tss more downstream (paired with Tss more upstream) 0.424242424242424 0.254761822734696 0.607846983812115 0.486850241664797 14 19 0.928661823272706 FALSE +health cancer tts Tts more downstream (paired with Tts more upstream) 0.5 0.210944638239297 0.789055361760703 1 6 6 1 FALSE
--- a/test-data/test06_consequences_summary.tabular Tue May 30 08:39:23 2023 +0000 +++ b/test-data/test06_consequences_summary.tabular Fri Jun 02 10:27:16 2023 +0000 @@ -1,19 +1,19 @@ Comparison featureCompared switchConsequence nrGenesWithConsequences nrIsoWithConsequences -cancer vs health Intron -retention Intron retention gain 3 5 -cancer vs health Intron -retention Intron retention loss 9 11 -cancer vs health Isoform seq -similarity Length gain 11 17 -cancer vs health Isoform seq -similarity Length loss 15 26 -cancer vs health NMD -status NMD insensitive 1 3 -cancer vs health NMD -status NMD sensitive 2 2 -cancer vs health Tss Tss more downstream 19 30 -cancer vs health Tss Tss more upstream 14 29 -cancer vs health Tts Tts more downstream 6 13 -cancer vs health Tts Tts more upstream 6 8 -cancer vs health ORF +health vs cancer Intron +retention Intron retention gain 9 11 +health vs cancer Intron +retention Intron retention loss 3 5 +health vs cancer Isoform seq +similarity Length gain 15 26 +health vs cancer Isoform seq +similarity Length loss 11 17 +health vs cancer NMD +status NMD insensitive 2 2 +health vs cancer NMD +status NMD sensitive 1 3 +health vs cancer Tss Tss more downstream 14 29 +health vs cancer Tss Tss more upstream 19 30 +health vs cancer Tts Tts more downstream 6 8 +health vs cancer Tts Tts more upstream 6 13 +health vs cancer ORF genomic Any consequence 0 0
--- a/test-data/test06_splicing_enrichment.tabular Tue May 30 08:39:23 2023 +0000 +++ b/test-data/test06_splicing_enrichment.tabular Fri Jun 02 10:27:16 2023 +0000 @@ -1,22 +1,22 @@ condition_1 condition_2 AStype nUp nDown propUp propUpCiLo propUpCiHi propUpPval propUpQval Significant Comparison -cancer health A3 gain (paired with A3 loss) 15 8 0.652173913043478 0.427343963036494 0.83623640162505 0.210039615631104 0.367569327354431 FALSE cancer +health cancer A3 gain (paired with A3 loss) 8 15 0.347826086956522 0.16376359837495 0.572656036963506 0.210039615631104 0.367569327354431 FALSE health vs -health -cancer health A5 gain (paired with A5 loss) 9 6 0.6 0.322869766206282 0.836635676140487 0.60723876953125 0.60723876953125 FALSE cancer +cancer +health cancer A5 gain (paired with A5 loss) 6 9 0.4 0.163364323859513 0.677130233793718 0.60723876953125 0.60723876953125 FALSE health vs -health -cancer health ATSS gain (paired with ATSS loss) 19 13 0.59375 0.406449246576476 0.763015899448257 0.377085587475449 0.495082259178162 FALSE cancer +cancer +health cancer ATSS gain (paired with ATSS loss) 13 19 0.40625 0.236984100551743 0.593550753423524 0.377085587475449 0.495082259178162 FALSE health vs -health -cancer health ATTS gain (paired with ATTS loss) 4 11 0.266666666666667 0.0778715462910436 0.551003241036971 0.11846923828125 0.340657552083334 FALSE cancer +cancer +health cancer ATTS gain (paired with ATTS loss) 11 4 0.733333333333333 0.448996758963029 0.922128453708956 0.11846923828125 0.340657552083334 FALSE health vs -health -cancer health ES (paired with EI) 10 15 0.4 0.211254806465142 0.61334650374316 0.42435622215271 0.495082259178162 FALSE cancer +cancer +health cancer ES (paired with EI) 15 10 0.6 0.38665349625684 0.788745193534858 0.42435622215271 0.495082259178162 FALSE health vs -health -cancer health IR gain (paired with IR loss) 3 9 0.25 0.0548606445279928 0.571858461878189 0.14599609375 0.340657552083334 FALSE cancer +cancer +health cancer IR gain (paired with IR loss) 9 3 0.75 0.428141538121811 0.945139355472007 0.14599609375 0.340657552083334 FALSE health vs -health -cancer health MES (paired with MEI) 2 8 0.2 0.0252107263268334 0.556095462307641 0.109375 0.340657552083334 FALSE cancer +cancer +health cancer MES (paired with MEI) 8 2 0.8 0.443904537692359 0.974789273673167 0.109375 0.340657552083334 FALSE health vs -health +cancer
--- a/test-data/test06_splicing_summary.tabular Tue May 30 08:39:23 2023 +0000 +++ b/test-data/test06_splicing_summary.tabular Fri Jun 02 10:27:16 2023 +0000 @@ -1,17 +1,17 @@ Comparison AStype splicingResult nrGenesWithConsequences nrIsoWithConsequences -cancer vs health A3 A3 in isoform used less 16 19 -cancer vs health A3 A3 in isoform used more 23 30 -cancer vs health A5 A5 in isoform used less 11 13 -cancer vs health A5 A5 in isoform used more 14 16 -cancer vs health ATSS ATSS in isoform used less 20 26 -cancer vs health ATSS ATSS in isoform used more 26 34 -cancer vs health ATTS ATTS in isoform used less 14 14 -cancer vs health ATTS ATTS in isoform used more 6 6 -cancer vs health ES ES in isoform used less 28 32 -cancer vs health ES ES in isoform used more 21 25 -cancer vs health IR IR in isoform used less 10 10 -cancer vs health IR IR in isoform used more 3 4 -cancer vs health MEE MEE in isoform used less 0 0 -cancer vs health MEE MEE in isoform used more 0 0 -cancer vs health MES MES in isoform used less 9 10 -cancer vs health MES MES in isoform used more 3 5 +health vs cancer A3 A3 in isoform used less 23 30 +health vs cancer A3 A3 in isoform used more 16 19 +health vs cancer A5 A5 in isoform used less 14 16 +health vs cancer A5 A5 in isoform used more 11 13 +health vs cancer ATSS ATSS in isoform used less 26 34 +health vs cancer ATSS ATSS in isoform used more 20 26 +health vs cancer ATTS ATTS in isoform used less 6 6 +health vs cancer ATTS ATTS in isoform used more 14 14 +health vs cancer ES ES in isoform used less 21 25 +health vs cancer ES ES in isoform used more 28 32 +health vs cancer IR IR in isoform used less 3 4 +health vs cancer IR IR in isoform used more 10 10 +health vs cancer MEE MEE in isoform used less 0 0 +health vs cancer MEE MEE in isoform used more 0 0 +health vs cancer MES MES in isoform used less 3 5 +health vs cancer MES MES in isoform used more 9 10
--- a/test-data/test06_switching.tabular Tue May 30 08:39:23 2023 +0000 +++ b/test-data/test06_switching.tabular Fri Jun 02 10:27:16 2023 +0000 @@ -1,55 +1,55 @@ gene_ref gene_id gene_name condition_1 condition_2 gene_switch_q_value switchConsequencesGene Rank -geneComp_00000066 CLSTN1 CLSTN1 cancer health 2.63840734749711e-51 FALSE 1 -geneComp_00000167 NADK NADK cancer health 5.98021460938895e-40 TRUE 2 -geneComp_00000210 PRKCZ PRKCZ cancer health 4.18324640310234e-37 TRUE 3 -geneComp_00000222 RPL11 RPL11 cancer health 2.39911661782576e-29 TRUE 4 -geneComp_00000227 SDF4 SDF4 cancer health 2.62564234344567e-28 TRUE 5 -geneComp_00000243 SRRM1 SRRM1 cancer health 7.11497254534458e-22 TRUE 6 -geneComp_00000017 ARHGEF10L ARHGEF10L cancer health 7.07643322536192e-20 TRUE 7 -geneComp_00000080 DVL1 DVL1 cancer health 2.7041623161036e-19 TRUE 8 -geneComp_00000138 KIF1B KIF1B cancer health 8.83353225639552e-16 TRUE 9 -geneComp_00000058 CDC2L1 CDC2L1 cancer health 5.02785283461027e-13 NA 10 -geneComp_00000019 ARHGEF19 ARHGEF19 cancer health 3.43190474162283e-12 TRUE 11 -geneComp_00000254 TMEM52 TMEM52 cancer health 9.43836095793092e-12 TRUE 12 -geneComp_00000101 FBXO44 FBXO44 cancer health 1.25146337218935e-11 TRUE 13 -geneComp_00000189 PER3 PER3 cancer health 2.618343550887e-11 TRUE 14 -geneComp_00000219 RERE RERE cancer health 9.86048379542823e-11 TRUE 15 -geneComp_00000003 ACAP3 ACAP3 cancer health 3.66320856918666e-08 TRUE 16 -geneComp_00000281 XLOC_000005 NA cancer health 6.83756168564135e-08 TRUE 17 -geneComp_00000301 XLOC_000129 NA cancer health 1.89169990108601e-07 TRUE 18 -geneComp_00000085 EIF4G3 EIF4G3 cancer health 9.53210349628728e-07 TRUE 19 -geneComp_00000277 WDR8 WDR8 cancer health 2.4050379356366e-06 TRUE 20 -geneComp_00000200 PLEKHG5 PLEKHG5 cancer health 2.65200395744161e-06 TRUE 21 -geneComp_00000165 MXRA8 MXRA8 cancer health 4.09018221463055e-06 TRUE 22 -geneComp_00000194 PIK3CD PIK3CD cancer health 4.26262542329329e-06 TRUE 23 -geneComp_00000118 HNRNPR HNRNPR cancer health 4.43094440336388e-06 NA 24 -geneComp_00000323 XLOC_001249 NA cancer health 5.97869364244676e-06 TRUE 25 -geneComp_00000342 XLOC_001353 NA cancer health 1.47897331984417e-05 TRUE 26 -geneComp_00000153 MIB2 MIB2 cancer health 1.85010676533132e-05 TRUE 27 -geneComp_00000004 ACOT7 ACOT7 cancer health 2.22089528793497e-05 TRUE 28 -geneComp_00000119 HP1BP3 HP1BP3 cancer health 3.95360727622295e-05 TRUE 29 -geneComp_00000352 ZBTB40 ZBTB40 cancer health 7.08120622533635e-05 FALSE 30 -geneComp_00000069 CROCC CROCC cancer health 0.00035468174423336 NA 31 -geneComp_00000142 LDLRAD2 LDLRAD2 cancer health 0.000443465792700213 TRUE 32 -geneComp_00000053 CASP9 CASP9 cancer health 0.0004985861544369 TRUE 33 -geneComp_00000077 DHRS3 DHRS3 cancer health 0.00050532341155672 TRUE 34 -geneComp_00000261 TNFRSF8 TNFRSF8 cancer health 0.00069495698171926 TRUE 35 -geneComp_00000267 UBE4B UBE4B cancer health 0.00069495698171926 TRUE 36 -geneComp_00000285 XLOC_000012 NA cancer health 0.00069495698171926 TRUE 37 -geneComp_00000083 ECE1 ECE1 cancer health 0.000730501167981291 TRUE 38 -geneComp_00000172 NIPAL3 NIPAL3 cancer health 0.000884959331769316 TRUE 39 -geneComp_00000252 TMEM201 TMEM201 cancer health 0.00130127619274632 TRUE 40 -geneComp_00000106 GALE GALE cancer health 0.00190711749673494 TRUE 41 -geneComp_00000056 CCNL2 CCNL2 cancer health 0.00213211505312704 TRUE 42 -geneComp_00000156 MMP23B MMP23B cancer health 0.00220763192701029 TRUE 43 -geneComp_00000223 RPL22 RPL22 cancer health 0.00414604315547501 TRUE 44 -geneComp_00000140 KLHL17 KLHL17 cancer health 0.0043156399415831 NA 45 -geneComp_00000131 KCNAB2 KCNAB2 cancer health 0.00450582195570915 TRUE 46 -geneComp_00000169 NBPF1 NBPF1 cancer health 0.00603768129678154 NA 47 -geneComp_00000132 KIAA0090 KIAA0090 cancer health 0.00637311306884828 NA 48 -geneComp_00000216 RCAN3 RCAN3 cancer health 0.00655117020038015 TRUE 49 -geneComp_00000160 MST1 MST1 cancer health 0.00970833700285509 TRUE 50 -geneComp_00000137 KIF17 KIF17 cancer health 0.020741914385789 TRUE 51 -geneComp_00000229 SFRS13A SFRS13A cancer health 0.035326111600384 TRUE 52 -geneComp_00000257 TNFRSF18 TNFRSF18 cancer health 0.0453089266879188 TRUE 53 -geneComp_00000256 TNFRSF14 TNFRSF14 cancer health 0.0490680824638558 TRUE 54 +geneComp_00000066 CLSTN1 CLSTN1 health cancer 2.64410644088928e-51 FALSE 1 +geneComp_00000167 NADK NADK health cancer 5.98941447943271e-40 TRUE 2 +geneComp_00000211 PRKCZ PRKCZ health cancer 4.19234377928155e-37 TRUE 3 +geneComp_00000222 RPL11 RPL11 health cancer 2.40166349917928e-29 TRUE 4 +geneComp_00000227 SDF4 SDF4 health cancer 2.62686121150453e-28 TRUE 5 +geneComp_00000243 SRRM1 SRRM1 health cancer 7.12163856022447e-22 TRUE 6 +geneComp_00000017 ARHGEF10L ARHGEF10L health cancer 7.07867901708182e-20 TRUE 7 +geneComp_00000080 DVL1 DVL1 health cancer 2.70521178079768e-19 TRUE 8 +geneComp_00000138 KIF1B KIF1B health cancer 8.83726654445401e-16 TRUE 9 +geneComp_00000058 CDC2L1 CDC2L1 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4.26320155401772e-06 TRUE 23 +geneComp_00000118 HNRNPR HNRNPR health cancer 4.43221576635977e-06 NA 24 +geneComp_00000323 XLOC_001249 NA health cancer 5.97838525068751e-06 TRUE 25 +geneComp_00000342 XLOC_001353 NA health cancer 1.47907485250366e-05 TRUE 26 +geneComp_00000153 MIB2 MIB2 health cancer 1.85029150590669e-05 TRUE 27 +geneComp_00000004 ACOT7 ACOT7 health cancer 2.22113863160212e-05 TRUE 28 +geneComp_00000119 HP1BP3 HP1BP3 health cancer 3.95403316047476e-05 TRUE 29 +geneComp_00000352 ZBTB40 ZBTB40 health cancer 7.08181153387625e-05 FALSE 30 +geneComp_00000070 CROCC CROCC health cancer 0.000354693426715386 NA 31 +geneComp_00000142 LDLRAD2 LDLRAD2 health cancer 0.000443477951686821 TRUE 32 +geneComp_00000053 CASP9 CASP9 health cancer 0.000498569105228876 TRUE 33 +geneComp_00000077 DHRS3 DHRS3 health cancer 0.000505307257030131 TRUE 34 +geneComp_00000261 TNFRSF8 TNFRSF8 health cancer 0.000695023031569716 TRUE 35 +geneComp_00000267 UBE4B UBE4B health cancer 0.000695023031569716 TRUE 36 +geneComp_00000285 XLOC_000012 NA health cancer 0.000695023031569716 TRUE 37 +geneComp_00000083 ECE1 ECE1 health cancer 0.000730501167953518 TRUE 38 +geneComp_00000172 NIPAL3 NIPAL3 health cancer 0.000885010728182188 TRUE 39 +geneComp_00000252 TMEM201 TMEM201 health cancer 0.0013013632641213 TRUE 40 +geneComp_00000106 GALE GALE health cancer 0.00190719809448641 TRUE 41 +geneComp_00000056 CCNL2 CCNL2 health cancer 0.00213228492084286 TRUE 42 +geneComp_00000156 MMP23B MMP23B health cancer 0.00220758083339994 TRUE 43 +geneComp_00000223 RPL22 RPL22 health cancer 0.00414628969828759 TRUE 44 +geneComp_00000140 KLHL17 KLHL17 health cancer 0.00431590225827285 NA 45 +geneComp_00000131 KCNAB2 KCNAB2 health cancer 0.00450586916304406 TRUE 46 +geneComp_00000169 NBPF1 NBPF1 health cancer 0.00603778731926021 NA 47 +geneComp_00000132 KIAA0090 KIAA0090 health cancer 0.00637359750073025 NA 48 +geneComp_00000216 RCAN3 RCAN3 health cancer 0.00655116094067907 TRUE 49 +geneComp_00000160 MST1 MST1 health cancer 0.00970828377249836 TRUE 50 +geneComp_00000137 KIF17 KIF17 health cancer 0.0207423127743009 TRUE 51 +geneComp_00000229 SFRS13A SFRS13A health cancer 0.0353266628185764 TRUE 52 +geneComp_00000257 TNFRSF18 TNFRSF18 health cancer 0.0453089882007119 TRUE 53 +geneComp_00000256 TNFRSF14 TNFRSF14 health cancer 0.0490679269744407 TRUE 54