| Previous changeset 4:512d6462f2ce (2023-05-30) Next changeset 6:298d81e5e138 (2023-12-20) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/isoformswitchanalyzer commit 7b7d9892618706dad95641831db8b9f83deb86e1 |
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modified:
IsoformSwitchAnalyzeR.R isoformswitchanalyzer.xml macros.xml test-data/test01.RData test-data/test02_counts.tabular test-data/test02_samples_annotation.tabular test-data/test03_cancer_counts.tabular test-data/test03_health_counts.tabular test-data/test04.RData test-data/test04_summary.tabular test-data/test06_consequences_enrichment.tabular test-data/test06_consequences_summary.tabular test-data/test06_splicing_enrichment.tabular test-data/test06_splicing_summary.tabular test-data/test06_switching.tabular test-data/test08_single_gene.pdf |
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added:
test-data/annotation_kallisto.gtf.gz test-data/kallisto_cond1_rep1.tsv test-data/kallisto_cond1_rep2.tsv test-data/kallisto_cond2_rep1.tsv test-data/kallisto_cond2_rep2.tsv test-data/test09.RData test-data/test10_samples_annotation.tabular test-data/transcriptome_kallisto.fasta.gz |
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| diff -r 512d6462f2ce -r b3f292d9f35d IsoformSwitchAnalyzeR.R --- a/IsoformSwitchAnalyzeR.R Tue May 30 08:39:23 2023 +0000 +++ b/IsoformSwitchAnalyzeR.R Fri Jun 02 10:27:16 2023 +0000 |
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| @@ -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 ) } |
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| diff -r 512d6462f2ce -r b3f292d9f35d isoformswitchanalyzer.xml --- a/isoformswitchanalyzer.xml Tue May 30 08:39:23 2023 +0000 +++ b/isoformswitchanalyzer.xml Fri Jun 02 10:27:16 2023 +0000 |
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| b'@@ -20,6 +20,9 @@\n description="An undefined error occurred, please check your input carefully and contact your administrator." />\n </stdio>\n <command><![CDATA[\n+ #set $conditions = list()\n+ #set $sampleIDs = list()\n+ #set $replicates = list()\n #if $functionMode.selector == \'data_import\'\n #if $functionMode.transcriptome.is_of_type("fasta.gz"):\n ln -s \'${functionMode.transcriptome}\' \'./transcriptome.fasta.gz\' &&\n@@ -51,21 +54,35 @@\n #set $stringtie_annotation = \'./stringtie_annotation.gtf\' \n #end if\n #end if\n+ #else if $functionMode.tool_source.selector == \'salmon\'\n+ #set $filename = \'quant.sf\'\n #else\n- #set $filename = \'quant.sf\'\n+ #set $filename = \'abundance.tsv\'\n #end if\n \n- #for $index in range(len($functionMode.first_factor.trans_counts)):\n- mkdir \'./input_files/${functionMode.first_factor.factorLevel}${index}/\' &&\n- ln -s $functionMode.first_factor.trans_counts[$index] \'./input_files/${functionMode.first_factor.factorLevel}${index}/${filename}\' &&\n+ #for $index in range(len($functionMode.tool_source.first_factor.trans_counts)):\n+ $conditions.append($functionMode.tool_source.first_factor.factorLevel)\n+ $sampleIDs.append(str($functionMode.tool_source.first_factor.factorLevel) + str($index))\n+ $replicates.append($index)\n+ mkdir \'./input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/\' &&\n+ ln -s $functionMode.tool_source.first_factor.trans_counts[$index] \'./input_files/${functionMode.tool_source.first_factor.factorLevel}${index}/${filename}\' &&\n #end for\n \n- #for $index in range(len($functionMode.second_factor.trans_counts)):\n- mkdir \'./input_files/${functionMode.second_factor.factorLevel}${index}/\' &&\n- ln -s $functionMode.second_factor.trans_counts[$index] \'./input_files/${functionMode.second_factor.factorLevel}${index}/${filename}\' &&\n+ #for $index in range(len($functionMode.tool_source.second_factor.trans_counts)):\n+ $conditions.append($functionMode.tool_source.second_factor.factorLevel)\n+ $sampleIDs.append(str($functionMode.tool_source.second_factor.factorLevel) + str($index))\n+ $replicates.append($index)\n+ mkdir \'./input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/\' &&\n+ ln -s $functionMode.tool_source.second_factor.trans_counts[$index] \'./input_files/${functionMode.tool_source.second_factor.factorLevel}${index}/${filename}\' &&\n #end for\n \n Rscript \'${__tool_directory__}/IsoformSwitchAnalyzeR.R\'\n+ #for $i, $condition in enumerate($conditions)\n+ --condition $condition\n+ --sampleID $sampleIDs[$i]\n+ --replicate $replicates[$i]\n+ #end for\n+ $functionMode.pairedSamples\n --modeSelector $functionMode.selector\n --parentDir \'./input_files\'\n --annotation $annotation\n@@ -207,31 +224,20 @@\n <option value="second_step">Analysis part two: Plot all isoform switches and their annotation</option>\n </param>\n <when value="data_import">\n- <section name="first_factor" title="1: Factor level" expanded="true">\n- <param name="factorLevel" type="text" value="FactorLevel" label="Specify a factor level, typical values could be \'tumor\' or \'treated\'"\n- help="Only letters, '..b'">\n- <element name="health0_dataset" file="test03_health_counts.tabular" ftype="tabular" lines_diff="6"/>\n+ <element name="cancer0_dataset" file="test03_cancer_counts.tabular" ftype="tabular" lines_diff="6"/>\n </output_collection>\n </test>\n <!-- Test 04: Extract isoform switches all outputs-->\n@@ -867,7 +875,7 @@\n </output>\n <output name="isoformFeatures" ftype="tabular">\n <assert_contents>\n- <has_size value="95185" delta="100"/>\n+ <has_size value="94888" delta="100"/>\n <has_text text="gene_overall_mean"/>\n </assert_contents>\n </output>\n@@ -1039,7 +1047,7 @@\n </output>\n <output name="isoformFeatures" ftype="tabular">\n <assert_contents>\n- <has_size value="99607" delta="50"/>\n+ <has_size value="99310" delta="50"/>\n <has_text text="gene_overall_mean"/>\n </assert_contents>\n </output>\n@@ -1061,6 +1069,54 @@\n </assert_contents>\n </output> \n </test>\n+ <!-- Test 09: Kallisto input-->\n+ <test expect_num_outputs="1">\n+ <conditional name="functionMode">\n+ <param name="selector" value="data_import"/>\n+ <param name="genomeAnnotation" value="annotation_kallisto.gtf.gz"/>\n+ <param name="transcriptome" value="transcriptome_kallisto.fasta.gz"/>\n+ <param name="countFiles" value="disabled"/>\n+ <conditional name="tool_source">\n+ <param name="selector" value="kallisto"/>\n+ <section name="first_factor">\n+ <param name="factorLevel" value="health"/>\n+ <param name="trans_counts" value="kallisto_cond1_rep1.tsv,kallisto_cond1_rep2.tsv"/>\n+ </section>\n+ <section name="second_factor">\n+ <param name="factorLevel" value="cancer"/>\n+ <param name="trans_counts" value="kallisto_cond2_rep1.tsv,kallisto_cond2_rep2.tsv"/>\n+ </section>\n+ </conditional>\n+ </conditional>\n+ <output name="switchList" file="test09.RData" ftype="rdata" compare="sim_size" delta="100"/>\n+ </test>\n+ <!-- Test 10: Test paired samples in the experimental design-->\n+ <test expect_num_outputs="3">\n+ <conditional name="functionMode">\n+ <param name="selector" value="data_import"/>\n+ <param name="genomeAnnotation" value="annotation_salmon.gtf.gz"/>\n+ <param name="transcriptome" value="transcriptome.fasta.gz"/>\n+ <param name="pairedSamples" value="true"/>\n+ <param name="countFiles" value="matrix"/>\n+ <conditional name="tool_source">\n+ <param name="selector" value="salmon"/>\n+ <section name="first_factor">\n+ <param name="factorLevel" value="health"/>\n+ <param name="trans_counts" value="salmon_cond1_rep1.sf,salmon_cond1_rep2.sf"/>\n+ </section>\n+ <section name="second_factor">\n+ <param name="factorLevel" value="cancer"/>\n+ <param name="trans_counts" value="salmon_cond2_rep1.sf,salmon_cond2_rep2.sf"/>\n+ </section>\n+ </conditional>\n+ </conditional>\n+ <output name="switchList" ftype="rdata">\n+ <assert_contents>\n+ <has_size value="652170" delta="300"/>\n+ </assert_contents>\n+ </output>\n+ <output name="sample_annotation" file="test10_samples_annotation.tabular" ftype="tabular"/>\n+ </test>\n </tests>\n <help><![CDATA[\n \n' |
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| diff -r 512d6462f2ce -r b3f292d9f35d macros.xml --- a/macros.xml Tue May 30 08:39:23 2023 +0000 +++ b/macros.xml Fri Jun 02 10:27:16 2023 +0000 |
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| @@ -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 |
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| diff -r 512d6462f2ce -r b3f292d9f35d test-data/annotation_kallisto.gtf.gz |
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| Binary file test-data/annotation_kallisto.gtf.gz has changed |
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| diff -r 512d6462f2ce -r b3f292d9f35d test-data/kallisto_cond1_rep1.tsv --- /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 |
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| @@ -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 |
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| diff -r 512d6462f2ce -r b3f292d9f35d test-data/kallisto_cond1_rep2.tsv --- /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 |
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| @@ -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 |
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| diff -r 512d6462f2ce -r b3f292d9f35d test-data/kallisto_cond2_rep1.tsv --- /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 |
| b |
| @@ -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 |
| b |
| diff -r 512d6462f2ce -r b3f292d9f35d test-data/kallisto_cond2_rep2.tsv --- /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 |
| b |
| @@ -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 |
| b |
| diff -r 512d6462f2ce -r b3f292d9f35d test-data/test01.RData |
| b |
| Binary file test-data/test01.RData has changed |
| b |
| diff -r 512d6462f2ce -r b3f292d9f35d test-data/test02_counts.tabular --- 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 |
| b |
| b'@@ -1,355 +1,355 @@\n-gene_names\tcancer0\tcancer1\thealth0\thealth1\n-AADACL3\t1.33294716142329\t1.60935135697703\t0\t0\n-AADACL4\t0.16565689184278\t0.245447543814652\t0\t0\n-ACAP3\t66.9545762637869\t99.4728681831285\t1393.95324090613\t1183.58827790662\n-ACOT7\t455.514031889104\t625.643253171647\t7395.10823740127\t2889.86502433136\n-ACTL8\t2.25786678564214\t2.8385206089638\t6.29646468356414\t9.65386190076367\n-AGMAT\t14.1868697001226\t20.8082199337387\t56.2113078807145\t41.8419006164206\n-AGRN\t223.424831149421\t331.946548429751\t2144.12485688125\t3783.10646304681\n-AGTRAP\t187.400533886563\t314.973593315019\t1943.78534029914\t2390.03265356525\n-AJAP1\t8.63047529957261\t13.8464275492248\t2.78718070452411\t0\n-AKR7A2\t83.7117317539189\t130.289924823431\t3829.83857542184\t3540.61290523654\n-AKR7A3\t1.86761600752251\t3.58107135446447\t19.1848890894377\t15.2519579815619\n-AKR7L\t1.63323529019925\t1.78518588259504\t12.0382831872031\t11.9429611381668\n-ALDH4A1\t80.0692491307954\t115.615849240505\t588.92974612004\t641.316225550933\n-ALPL\t598.739713486774\t931.026396105693\t12.5179727486086\t145.603586056744\n-ANGPTL7\t0.111187468282468\t0.164742599508691\t11.7533214949055\t12.3890347339164\n-APITD1\t27.9435627190935\t40.1067500091512\t802.720467188703\t663.18564778364\n-ARHGEF10L\t80.3813346280653\t125.687632167421\t575.337403596391\t982.752730025466\n-ARHGEF16\t44.2754028984311\t66.8497008399258\t8.93761413278206\t2.14380019716824\n-ARHGEF19\t115.733727841445\t189.932215231752\t192.61472131494\t216.922297485954\n-ASAP3\t88.368604104536\t144.185270660234\t977.339687032257\t832.468754427446\n-ATAD3A\t170.332210340393\t256.909438164756\t2909.59238880021\t1787.85567999184\n-ATAD3B\t115.009269719842\t186.922563175749\t1204.49289913673\t580.698972738788\n-ATAD3C\t9.18645892844685\t11.1689876678097\t20.3511517744843\t14.9657017546822\n-ATP13A2\t173.079288123976\t259.826155166127\t778.918736405516\t778.83424421371\n-AURKAIP1\t431.089374951588\t734.107961651523\t9367.79479097331\t6368.53564372911\n-B3GALT6\t34.5537089926203\t48.0941285791035\t1107.4652590036\t1344.53791709811\n-C1orf126\t0.748005384270891\t2.19315673139357\t0\t2.02937495588995\n-C1orf127\t0.219649529265469\t1.31728558966594\t0.73417113252224\t0\n-C1orf128\t157.021218105179\t205.564314627884\t2055.87258399552\t1840.70695418312\n-C1orf130\t0.270304535188066\t0.445000989755816\t0\t0.293709236838892\n-C1orf144\t169.905131358614\t236.936379177537\t6169.84439356059\t6172.79967616817\n-C1orf151\t81.934540083501\t106.83864564802\t2316.80019551674\t1742.26068228731\n-C1orf158\t0.306319741118665\t0\t0\t0\n-C1orf159\t25.4472609092091\t27.0936925692478\t255.003897423656\t260.387760636754\n-C1orf167\t0.852445327466635\t1.62734609336196\t4.28017084616318\t20.8037404760945\n-C1orf170\t1.12825925747856\t4.0128035997215\t42.2830759803238\t44.6208842491559\n-C1orf174\t65.3123327213875\t103.529715471474\t1150.25066664382\t1553.57631620601\n-C1orf187\t38.4882619397459\t66.6560127067159\t22.7498270005338\t2.90670998197146\n-C1orf200\t0.140010077377323\t0\t0\t0\n-C1orf201\t16.9572193953188\t29.7070533850009\t301.219367711266\t379.623514344136\n-C1orf211\t14.6209036697657\t26.998386277083\t1.41183164282385\t8.65855898698444\n-C1orf213\t0.518508587606857\t1.88619698952573\t76.5600381962453\t156.763728464001\n-C1orf222\t0.381237303744296\t0.529475492302115\t0\t0\n-C1orf70\t7.51184976845881\t19.8485556995299\t239.879629899723\t290.034472160915\n-C1orf86\t225.001393970245\t375.819392770559\t3491.25500640192\t2865.04772849532\n-C1orf89\t5.10917443855593\t12.0376749429161\t202.484599015937\t212.283237977287\n-C1orf93\t100.534745697611\t160.074553609957\t1576.8889615254\t1358.37868843451\n-CAD\t1.78359239559776\t5.00082342629287\t0\t13.4392425305562\n-CALML6\t2.92860771428337\t5.65982936080012\t0\t2.10905502038753\n-CAMK2N1\t14.2906082102419\t26.1322888570167\t8126.76185609601\t16305.1258047596\n-CAMTA1\t200.588720737929\t253.543060947236\t3055.15380157953\t4100.09091814611\n-CAPZB\t619.112320909139\t991.572432852428\t20316.4731362545\t24041.0162369706\n-CASP9\t51.1870965570691\t80.3510692413285\t340.999216471908\t304.57891159937\n-CASZ1\t13.6330268070182\t19.042062635585\t8.81866733613576\t9.75816312925625\n-CCDC27\t0.0573867205178809\t1.02033468450467\t0.75773394235314\t0\n-'..b'149588\t26.9427447128\t34.947787485532\n+XLOC_000129\t353.587071781866\t758.240294777622\t18.772462633958\t29.3468930311443\n+XLOC_000138\t202.53853151081\t344.095867778729\t38.8700741575041\t51.7940496915431\n+XLOC_000148\t2.54033057482786\t0.518381268897529\t1.57031994775796\t2.0703046333356\n+XLOC_000158\t0\t0\t1.63670091555161\t4.29047267335988\n+XLOC_000173\t0.669622554351972\t7.18675196052498\t1.06214651959231\t1.12407426258865\n+XLOC_000174\t3679.99023128108\t22568.9992411476\t529.705405954172\t9418.1343848515\n+XLOC_000179\t485.640103066908\t724.628699874925\t53.0677442654029\t80.9418864284067\n+XLOC_000187\t26.360772631746\t15.4131952005694\t1.0725849356793\t1.29123388065767\n+XLOC_000188\t2500.18608736872\t2893.71714995025\t485.665022302667\t730.200923926726\n+XLOC_000190\t0\t0\t0.114539036581279\t0.169708372845532\n+XLOC_001217\t2027.34232722767\t1140.52321249461\t130.676612377691\t209.33874703643\n+XLOC_001218\t9.52791266360871\t0\t1.11065103222938\t4.57113901513204\n+XLOC_001219\t11.3705108476242\t19.898838698614\t0.28644580395248\t0.462998956729158\n+XLOC_001220\t17.6627820045462\t27.9729729298378\t76.2580000478759\t118.977904648644\n+XLOC_001222\t87.3738347178654\t163.72394213182\t126.034325977775\t193.513860913044\n+XLOC_001223\t31341.9338316771\t0\t163547.84518143\t150008.962644156\n+XLOC_001225\t31341.9338316771\t0\t163547.84518143\t150008.962644156\n+XLOC_001227\t42.4480653881083\t73.0480407662068\t28.4239434935344\t44.1599898071085\n+XLOC_001228\t37.1746781190191\t53.9434758606289\t2.96779776535697\t2.72934466849826\n+XLOC_001230\t9.44420723023971\t7.24002040593887\t1.04098840207296\t0\n+XLOC_001235\t0\t0\t0.643193954521966\t1.20378544200498\n+XLOC_001241\t27.1926538485809\t19.1088966517602\t4.11476546544828\t7.20519927331771\n+XLOC_001249\t170.271058414378\t55.3105894310116\t9.59909351607688\t12.2964666116257\n+XLOC_001255\t656.756902666893\t1708.04361756199\t43.8864481692447\t57.2375911584504\n+XLOC_001261\t0\t0\t0.90538512843992\t1.62893626076707\n+XLOC_001262\t32.879450200818\t28.7871005595427\t2.57484095100331\t8.57724811776433\n+XLOC_001265\t260.853867089462\t140.036931233652\t102.124501928649\t178.840887319719\n+XLOC_001269\t10.1892351170661\t27.5651269941468\t0.11275216952578\t0.222119105968671\n+XLOC_001271\t0.739963735624112\t0\t0\t0\n+XLOC_001272\t3.40547383237821\t18.2746745328208\t0\t0\n+XLOC_001279\t0\t0\t0\t0.196093126802293\n+XLOC_001300\t61.2454109786738\t99.1536701126289\t29.1309548025757\t32.8750060677505\n+XLOC_001302\t48.8092380588883\t91.298890695025\t26.859308595584\t46.1638520055266\n+XLOC_001321\t2808.34205445117\t1561.66669448542\t304.286653369147\t352.220285459156\n+XLOC_001325\t223.97284590171\t244.287622687443\t38.3463137232589\t44.5659670836712\n+XLOC_001335\t5.3417274447352\t0.450899882954414\t0.500183500127258\t0.594266737589076\n+XLOC_001338\t28354.734013617\t17953.5236839171\t1730.03542846583\t3865.41697747869\n+XLOC_001339\t43.8346808379212\t47.6814554489967\t7.23103916627791\t10.251015971773\n+XLOC_001349\t51.1774249153872\t102.986302873693\t23.8440839846515\t29.2782663595089\n+XLOC_001350\t0.816249598627034\t1.00664968225117\t1.4752288850076\t2.1408032514761\n+XLOC_001351\t1407.51704323402\t2617.27714122475\t21.2015565220575\t33.3290832161605\n+XLOC_001353\t624.002928066391\t695.456434884007\t83.4951990071602\t149.319321757687\n+XLOC_001356\t230.807964129475\t606.651426727153\t50.2094341503045\t115.190039740662\n+XLOC_001372\t14.2153949190097\t24.2174693160748\t1.91582617937623\t2.83861034753068\n+XLOC_001379\t0\t5.64750205253292\t0.0910349755442975\t0.134883347719491\n+XLOC_001388\t0.70418227693387\t0.539833038602494\t0.0532721212125523\t0.236667522431167\n+XLOC_001389\t475.397331693707\t735.365654745429\t6.75542956098647\t11.622221273691\n+XLOC_001394\t0\t0\t0\t0.325668438290865\n+XLOC_001401\t0\t0\t0.184850759376464\t0.27372057669569\n+XLOC_001404\t84.3316006411086\t171.862029782374\t6.91245087404029\t18.7625395631549\n+ZBTB17\t792.615674949323\t724.307200079801\t39.465672732615\t62.8537160424089\n+ZBTB40\t225.002031996727\t308.369466259324\t36.5722648528181\t24.6063437546859\n+ZBTB48\t285.548786027533\t290.958457686854\t38.6672531811893\t60.54808278606\n+ZNF436\t381.877284921004\t509.309870434116\t1.88956101189413\t3.81408651722365\n' |
| b |
| diff -r 512d6462f2ce -r b3f292d9f35d test-data/test02_samples_annotation.tabular --- 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 |
| b |
| @@ -1,5 +1,5 @@ sampleID condition +health0 health +health1 health cancer0 cancer cancer1 cancer -health0 health -health1 health |
| b |
| diff -r 512d6462f2ce -r b3f292d9f35d test-data/test03_cancer_counts.tabular --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 512d6462f2ce -r b3f292d9f35d test-data/test03_health_counts.tabular --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 512d6462f2ce -r b3f292d9f35d test-data/test04.RData |
| b |
| Binary file test-data/test04.RData has changed |
| b |
| diff -r 512d6462f2ce -r b3f292d9f35d test-data/test04_summary.tabular --- 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 |
| b |
| @@ -1,2 +1,2 @@ Comparison nrIsoforms nrSwitches nrGenes -cancer vs health 91 70 54 +health vs cancer 91 70 54 |
| b |
| diff -r 512d6462f2ce -r b3f292d9f35d test-data/test06_consequences_enrichment.tabular --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 512d6462f2ce -r b3f292d9f35d test-data/test06_consequences_summary.tabular --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 512d6462f2ce -r b3f292d9f35d test-data/test06_splicing_enrichment.tabular --- 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 |
| b |
| @@ -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 |
| b |
| diff -r 512d6462f2ce -r b3f292d9f35d test-data/test06_splicing_summary.tabular --- 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 |
| b |
| @@ -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 |
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| diff -r 512d6462f2ce -r b3f292d9f35d test-data/test06_switching.tabular --- 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 |
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| b'@@ -1,55 +1,55 @@\n gene_ref\tgene_id\tgene_name\tcondition_1\tcondition_2\tgene_switch_q_value\tswitchConsequencesGene\tRank\n-geneComp_00000066\tCLSTN1\tCLSTN1\tcancer\thealth\t2.63840734749711e-51\tFALSE\t1\n-geneComp_00000167\tNADK\tNADK\tcancer\thealth\t5.98021460938895e-40\tTRUE\t2\n-geneComp_00000210\tPRKCZ\tPRKCZ\tcancer\thealth\t4.18324640310234e-37\tTRUE\t3\n-geneComp_00000222\tRPL11\tRPL11\tcancer\thealth\t2.39911661782576e-29\tTRUE\t4\n-geneComp_00000227\tSDF4\tSDF4\tcancer\thealth\t2.62564234344567e-28\tTRUE\t5\n-geneComp_00000243\tSRRM1\tSRRM1\tcancer\thealth\t7.11497254534458e-22\tTRUE\t6\n-geneComp_00000017\tARHGEF10L\tARHGEF10L\tcancer\thealth\t7.07643322536192e-20\tTRUE\t7\n-geneComp_00000080\tDVL1\tDVL1\tcancer\thealth\t2.7041623161036e-19\tTRUE\t8\n-geneComp_00000138\tKIF1B\tKIF1B\tcancer\thealth\t8.83353225639552e-16\tTRUE\t9\n-geneComp_00000058\tCDC2L1\tCDC2L1\tcancer\thealth\t5.02785283461027e-13\tNA\t10\n-geneComp_00000019\tARHGEF19\tARHGEF19\tcancer\thealth\t3.43190474162283e-12\tTRUE\t11\n-geneComp_00000254\tTMEM52\tTMEM52\tcancer\thealth\t9.43836095793092e-12\tTRUE\t12\n-geneComp_00000101\tFBXO44\tFBXO44\tcancer\thealth\t1.25146337218935e-11\tTRUE\t13\n-geneComp_00000189\tPER3\tPER3\tcancer\thealth\t2.618343550887e-11\tTRUE\t14\n-geneComp_00000219\tRERE\tRERE\tcancer\thealth\t9.86048379542823e-11\tTRUE\t15\n-geneComp_00000003\tACAP3\tACAP3\tcancer\thealth\t3.66320856918666e-08\tTRUE\t16\n-geneComp_00000281\tXLOC_000005\tNA\tcancer\thealth\t6.83756168564135e-08\tTRUE\t17\n-geneComp_00000301\tXLOC_000129\tNA\tcancer\thealth\t1.89169990108601e-07\tTRUE\t18\n-geneComp_00000085\tEIF4G3\tEIF4G3\tcancer\thealth\t9.53210349628728e-07\tTRUE\t19\n-geneComp_00000277\tWDR8\tWDR8\tcancer\thealth\t2.4050379356366e-06\tTRUE\t20\n-geneComp_00000200\tPLEKHG5\tPLEKHG5\tcancer\thealth\t2.65200395744161e-06\tTRUE\t21\n-geneComp_00000165\tMXRA8\tMXRA8\tcancer\thealth\t4.09018221463055e-06\tTRUE\t22\n-geneComp_00000194\tPIK3CD\tPIK3CD\tcancer\thealth\t4.26262542329329e-06\tTRUE\t23\n-geneComp_00000118\tHNRNPR\tHNRNPR\tcancer\thealth\t4.43094440336388e-06\tNA\t24\n-geneComp_00000323\tXLOC_001249\tNA\tcancer\thealth\t5.97869364244676e-06\tTRUE\t25\n-geneComp_00000342\tXLOC_001353\tNA\tcancer\thealth\t1.47897331984417e-05\tTRUE\t26\n-geneComp_00000153\tMIB2\tMIB2\tcancer\thealth\t1.85010676533132e-05\tTRUE\t27\n-geneComp_00000004\tACOT7\tACOT7\tcancer\thealth\t2.22089528793497e-05\tTRUE\t28\n-geneComp_00000119\tHP1BP3\tHP1BP3\tcancer\thealth\t3.95360727622295e-05\tTRUE\t29\n-geneComp_00000352\tZBTB40\tZBTB40\tcancer\thealth\t7.08120622533635e-05\tFALSE\t30\n-geneComp_00000069\tCROCC\tCROCC\tcancer\thealth\t0.00035468174423336\tNA\t31\n-geneComp_00000142\tLDLRAD2\tLDLRAD2\tcancer\thealth\t0.000443465792700213\tTRUE\t32\n-geneComp_00000053\tCASP9\tCASP9\tcancer\thealth\t0.0004985861544369\tTRUE\t33\n-geneComp_00000077\tDHRS3\tDHRS3\tcancer\thealth\t0.00050532341155672\tTRUE\t34\n-geneComp_00000261\tTNFRSF8\tTNFRSF8\tcancer\thealth\t0.00069495698171926\tTRUE\t35\n-geneComp_00000267\tUBE4B\tUBE4B\tcancer\thealth\t0.00069495698171926\tTRUE\t36\n-geneComp_00000285\tXLOC_000012\tNA\tcancer\thealth\t0.00069495698171926\tTRUE\t37\n-geneComp_00000083\tECE1\tECE1\tcancer\thealth\t0.000730501167981291\tTRUE\t38\n-geneComp_00000172\tNIPAL3\tNIPAL3\tcancer\thealth\t0.000884959331769316\tTRUE\t39\n-geneComp_00000252\tTMEM201\tTMEM201\tcancer\thealth\t0.00130127619274632\tTRUE\t40\n-geneComp_00000106\tGALE\tGALE\tcancer\thealth\t0.00190711749673494\tTRUE\t41\n-geneComp_00000056\tCCNL2\tCCNL2\tcancer\thealth\t0.00213211505312704\tTRUE\t42\n-geneComp_00000156\tMMP23B\tMMP23B\tcancer\thealth\t0.00220763192701029\tTRUE\t43\n-geneComp_00000223\tRPL22\tRPL22\tcancer\thealth\t0.00414604315547501\tTRUE\t44\n-geneComp_00000140\tKLHL17\tKLHL17\tcancer\thealth\t0.0043156399415831\tNA\t45\n-geneComp_00000131\tKCNAB2\tKCNAB2\tcancer\thealth\t0.00450582195570915\tTRUE\t46\n-geneComp_00000169\tNBPF1\tNBPF1\tcancer\thealth\t0.00603768129678154\tNA\t47\n-geneComp_00000132\tKIAA0090\tKIAA0090\tcancer\thealth\t0.00637311306884828\tNA\t48\n-geneComp_00000216\tRCAN3\tRCAN3\tcancer\thealth\t0.00655117020038015\tTRUE\t49\n-geneComp_00000160\tMST1\tMST1\tcancer\thealth\t0.00970833700285509\tTRUE\t50\n-geneComp_00000137\tKIF17\tKIF17\tcancer\thealth\t0.020741914385789\tTRUE\t51\n-geneComp_00000229\tSFRS13A\tSFRS13A\tcancer\thealth\t0.035326111600384\tTRUE\t52\n-geneComp_00000257\tT'..b'N1\thealth\tcancer\t2.64410644088928e-51\tFALSE\t1\n+geneComp_00000167\tNADK\tNADK\thealth\tcancer\t5.98941447943271e-40\tTRUE\t2\n+geneComp_00000211\tPRKCZ\tPRKCZ\thealth\tcancer\t4.19234377928155e-37\tTRUE\t3\n+geneComp_00000222\tRPL11\tRPL11\thealth\tcancer\t2.40166349917928e-29\tTRUE\t4\n+geneComp_00000227\tSDF4\tSDF4\thealth\tcancer\t2.62686121150453e-28\tTRUE\t5\n+geneComp_00000243\tSRRM1\tSRRM1\thealth\tcancer\t7.12163856022447e-22\tTRUE\t6\n+geneComp_00000017\tARHGEF10L\tARHGEF10L\thealth\tcancer\t7.07867901708182e-20\tTRUE\t7\n+geneComp_00000080\tDVL1\tDVL1\thealth\tcancer\t2.70521178079768e-19\tTRUE\t8\n+geneComp_00000138\tKIF1B\tKIF1B\thealth\tcancer\t8.83726654445401e-16\tTRUE\t9\n+geneComp_00000058\tCDC2L1\tCDC2L1\thealth\tcancer\t5.03054678789216e-13\tNA\t10\n+geneComp_00000019\tARHGEF19\tARHGEF19\thealth\tcancer\t3.4315648279622e-12\tTRUE\t11\n+geneComp_00000254\tTMEM52\tTMEM52\thealth\tcancer\t9.44090558511571e-12\tTRUE\t12\n+geneComp_00000101\tFBXO44\tFBXO44\thealth\tcancer\t1.25165679599995e-11\tTRUE\t13\n+geneComp_00000189\tPER3\tPER3\thealth\tcancer\t2.61831084358402e-11\tTRUE\t14\n+geneComp_00000219\tRERE\tRERE\thealth\tcancer\t9.86352533538375e-11\tTRUE\t15\n+geneComp_00000003\tACAP3\tACAP3\thealth\tcancer\t3.66457649115483e-08\tTRUE\t16\n+geneComp_00000281\tXLOC_000005\tNA\thealth\tcancer\t6.83649414759608e-08\tTRUE\t17\n+geneComp_00000301\tXLOC_000129\tNA\thealth\tcancer\t1.89184197326376e-07\tTRUE\t18\n+geneComp_00000085\tEIF4G3\tEIF4G3\thealth\tcancer\t9.53358521970902e-07\tTRUE\t19\n+geneComp_00000277\tWDR8\tWDR8\thealth\tcancer\t2.40546450275541e-06\tTRUE\t20\n+geneComp_00000201\tPLEKHG5\tPLEKHG5\thealth\tcancer\t2.65208735288124e-06\tTRUE\t21\n+geneComp_00000165\tMXRA8\tMXRA8\thealth\tcancer\t4.09014496081351e-06\tTRUE\t22\n+geneComp_00000195\tPIK3CD\tPIK3CD\thealth\tcancer\t4.26320155401772e-06\tTRUE\t23\n+geneComp_00000118\tHNRNPR\tHNRNPR\thealth\tcancer\t4.43221576635977e-06\tNA\t24\n+geneComp_00000323\tXLOC_001249\tNA\thealth\tcancer\t5.97838525068751e-06\tTRUE\t25\n+geneComp_00000342\tXLOC_001353\tNA\thealth\tcancer\t1.47907485250366e-05\tTRUE\t26\n+geneComp_00000153\tMIB2\tMIB2\thealth\tcancer\t1.85029150590669e-05\tTRUE\t27\n+geneComp_00000004\tACOT7\tACOT7\thealth\tcancer\t2.22113863160212e-05\tTRUE\t28\n+geneComp_00000119\tHP1BP3\tHP1BP3\thealth\tcancer\t3.95403316047476e-05\tTRUE\t29\n+geneComp_00000352\tZBTB40\tZBTB40\thealth\tcancer\t7.08181153387625e-05\tFALSE\t30\n+geneComp_00000070\tCROCC\tCROCC\thealth\tcancer\t0.000354693426715386\tNA\t31\n+geneComp_00000142\tLDLRAD2\tLDLRAD2\thealth\tcancer\t0.000443477951686821\tTRUE\t32\n+geneComp_00000053\tCASP9\tCASP9\thealth\tcancer\t0.000498569105228876\tTRUE\t33\n+geneComp_00000077\tDHRS3\tDHRS3\thealth\tcancer\t0.000505307257030131\tTRUE\t34\n+geneComp_00000261\tTNFRSF8\tTNFRSF8\thealth\tcancer\t0.000695023031569716\tTRUE\t35\n+geneComp_00000267\tUBE4B\tUBE4B\thealth\tcancer\t0.000695023031569716\tTRUE\t36\n+geneComp_00000285\tXLOC_000012\tNA\thealth\tcancer\t0.000695023031569716\tTRUE\t37\n+geneComp_00000083\tECE1\tECE1\thealth\tcancer\t0.000730501167953518\tTRUE\t38\n+geneComp_00000172\tNIPAL3\tNIPAL3\thealth\tcancer\t0.000885010728182188\tTRUE\t39\n+geneComp_00000252\tTMEM201\tTMEM201\thealth\tcancer\t0.0013013632641213\tTRUE\t40\n+geneComp_00000106\tGALE\tGALE\thealth\tcancer\t0.00190719809448641\tTRUE\t41\n+geneComp_00000056\tCCNL2\tCCNL2\thealth\tcancer\t0.00213228492084286\tTRUE\t42\n+geneComp_00000156\tMMP23B\tMMP23B\thealth\tcancer\t0.00220758083339994\tTRUE\t43\n+geneComp_00000223\tRPL22\tRPL22\thealth\tcancer\t0.00414628969828759\tTRUE\t44\n+geneComp_00000140\tKLHL17\tKLHL17\thealth\tcancer\t0.00431590225827285\tNA\t45\n+geneComp_00000131\tKCNAB2\tKCNAB2\thealth\tcancer\t0.00450586916304406\tTRUE\t46\n+geneComp_00000169\tNBPF1\tNBPF1\thealth\tcancer\t0.00603778731926021\tNA\t47\n+geneComp_00000132\tKIAA0090\tKIAA0090\thealth\tcancer\t0.00637359750073025\tNA\t48\n+geneComp_00000216\tRCAN3\tRCAN3\thealth\tcancer\t0.00655116094067907\tTRUE\t49\n+geneComp_00000160\tMST1\tMST1\thealth\tcancer\t0.00970828377249836\tTRUE\t50\n+geneComp_00000137\tKIF17\tKIF17\thealth\tcancer\t0.0207423127743009\tTRUE\t51\n+geneComp_00000229\tSFRS13A\tSFRS13A\thealth\tcancer\t0.0353266628185764\tTRUE\t52\n+geneComp_00000257\tTNFRSF18\tTNFRSF18\thealth\tcancer\t0.0453089882007119\tTRUE\t53\n+geneComp_00000256\tTNFRSF14\tTNFRSF14\thealth\tcancer\t0.0490679269744407\tTRUE\t54\n' 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| diff -r 512d6462f2ce -r b3f292d9f35d test-data/test08_single_gene.pdf |
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| diff -r 512d6462f2ce -r b3f292d9f35d test-data/test09.RData |
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| diff -r 512d6462f2ce -r b3f292d9f35d test-data/test10_samples_annotation.tabular --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/test10_samples_annotation.tabular Fri Jun 02 10:27:16 2023 +0000 |
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| @@ -0,0 +1,5 @@ +sampleID condition replicate +health0 health 0 +health1 health 1 +cancer0 cancer 0 +cancer1 cancer 1 |
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| diff -r 512d6462f2ce -r b3f292d9f35d test-data/transcriptome_kallisto.fasta.gz |
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