| Previous changeset 1:405e436ec8b3 (2016-11-18) Next changeset 3:4ffe49475169 (2016-12-13) |
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Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 30192223eeb60f33a42046921351c6ba3c80c90c |
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added:
test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.depleted test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.enriched test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched test-data/count/analyze_diff_expr/results.matrix test-data/count/analyze_diff_expr/results.matrix.RData test-data/count/analyze_diff_expr/results.matrix.log2.centered.dat test-data/count/analyze_diff_expr/results.matrix.log2.centered.genes_vs_samples_heatmap.pdf test-data/count/analyze_diff_expr/results.matrix.log2.dat test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor.dat test-data/count/analyze_diff_expr/results.matrix.log2.sample_cor_matrix.pdf test-data/count/trinotate/genes.lengths.txt test-data/count/trinotate/go_annotations.txt |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset Mon Nov 21 09:22:49 2016 -0500 |
| b |
| @@ -0,0 +1,7 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR4277|c0_g1_i1 3852.97388871986 161.116814813422 2007.04535176664 -4.57259674791206 0.121601866332754 -37.6030145409076 0 0 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR4761|c0_g1_i1 1645.20640957447 193.196157329029 919.201283451752 -3.08847487551254 0.143642016580712 -21.5011940728159 1.51733402752078e-102 1.66906743027286e-101 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR2107|c1_g1_i1 48.9228907410258 7.40521775805688 28.1640542495414 -2.6949883047084 0.431525668867458 -6.24525607429428 4.23106352657394e-10 1.55138995974378e-09 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR2672|c0_g1_i1 18.3155337236093 2.26581902751323 10.2906763755613 -2.88818323474529 0.724350842979802 -3.98727117216294 6.68376171815065e-05 0.000157545811927837 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00 +TR127|c1_g1_i1 13.461799216177 1.21881296083961 7.34030608850831 -3.33218181130749 0.914685635912973 -3.64298036448506 0.000269499403689035 0.000576210779000196 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR5055|c0_g2_i1 23.3590211688541 5.52768338415684 14.4433522765055 -2.04478780320925 0.562727305023446 -3.63370994255211 0.00027937492315161 0.000576210779000196 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00 |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted Mon Nov 21 09:22:49 2016 -0500 |
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| @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched Mon Nov 21 09:22:49 2016 -0500 |
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| @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset Mon Nov 21 09:22:49 2016 -0500 |
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| @@ -0,0 +1,4 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR131|c0_g1_i1 26.1866396538608 1340.30918254958 683.247911101723 5.67372481552909 0.187406695960058 30.274931140872 2.45144211418965e-201 4.04487948841292e-200 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR3091|c0_g1_i1 16.7444693227929 328.569936894811 172.657203108802 4.29039998257063 0.240421038467916 17.8453599980735 3.14072644239509e-71 2.59109931497595e-70 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR3788|c0_g1_i1 19.5075441237117 134.95369713876 77.2306206312357 2.77038513264018 0.262760026053246 10.5434040871909 5.44900939296595e-26 2.56881871382681e-25 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00 |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.depleted --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.depleted Mon Nov 21 09:22:49 2016 -0500 |
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| @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.enriched --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_GSNO.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset.GOseq.enriched Mon Nov 21 09:22:49 2016 -0500 |
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| @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset Mon Nov 21 09:22:49 2016 -0500 |
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| @@ -0,0 +1,7 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR4277|c0_g1_i1 4705.34614971641 162.902721493704 2434.12443560506 -4.84860951090545 0.124597307945428 -38.9142397284305 0 0 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR4761|c0_g1_i1 2012.6141923276 384.620292965437 1198.61724264652 -2.38450946693381 0.143863830576436 -16.5747669680385 1.06073316501088e-61 1.34359534234711e-60 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR2107|c1_g1_i1 59.5986596731862 1.89840873462066 30.7485342039034 -4.81058600791914 0.641850436461167 -7.49487066557473 6.63637683134955e-14 2.29256654173894e-13 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR127|c1_g1_i1 16.3791628279609 1.58772512712498 8.98344397754296 -3.19771077466237 0.834376974262452 -3.83245328346816 0.00012687169720824 0.000267840249661839 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR1894|c2_g1_i1 16.2826445742552 1.67571344127509 8.97917900776516 -3.15659686337855 0.834779400611257 -3.7813545244015 0.00015597736029041 0.000307529893573321 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00 +TR5055|c0_g2_i1 28.6665933385886 6.05959103586122 17.3630921872249 -2.17768048931004 0.577307428800381 -3.77213314894485 0.000161857838722801 0.000307529893573321 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00 |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.depleted Mon Nov 21 09:22:49 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_37-UP.subset.GOseq.enriched Mon Nov 21 09:22:49 2016 -0500 |
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| @@ -0,0 +1,2 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR go_term +GO:0008270 0.0469428206943769 0.996332779511344 3 6 zinc ion binding MF 0.790651800018629 MF zinc ion binding |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset Mon Nov 21 09:22:49 2016 -0500 |
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| @@ -0,0 +1,5 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR131|c0_g1_i1 32.0461070493257 1436.30905989883 734.177583474076 5.48367743370229 0.196017912869615 27.9753893581648 3.23827538807456e-172 6.15272323734167e-171 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR3091|c0_g1_i1 20.4914097091341 321.651020117047 171.071214913091 3.96886910507283 0.256323110469072 15.4838519937191 4.45952081812589e-54 4.2365447772196e-53 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR2779|c0_g1_i1 191.51955185349 1058.15934185376 624.839446853626 2.46616535412611 0.177102083131526 13.9251064161374 4.4587691300744e-44 3.38866453885655e-43 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TR5075|c0_g1_i1 19.3833722195684 136.98672801182 78.1850501156942 2.80049241151413 0.293976352213923 9.52625063350759 1.63066468983638e-21 8.85217974482605e-21 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00 |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted Mon Nov 21 09:22:49 2016 -0500 |
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| @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_37_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched Mon Nov 21 09:22:49 2016 -0500 |
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| @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_GSNO-UP.subset Mon Nov 21 09:22:49 2016 -0500 |
| b |
| @@ -0,0 +1,1 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset Mon Nov 21 09:22:49 2016 -0500 |
| b |
| @@ -0,0 +1,3 @@ +id baseMeanA baseMeanB baseMean log2FoldChange lfcSE stat pvalue padj wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR2779|c0_g1_i1 195.849684476753 966.924129135581 581.386906806167 2.25621220756415 0.156114979193812 14.4522467940961 2.42639762934434e-47 5.82335431042642e-46 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TR24|c0_g1_i1 39.3724575919554 183.288101009647 111.330279300801 2.11680322693425 0.240338854880295 8.80757806717753 1.27878744153922e-18 7.67272464923531e-18 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.depleted Mon Nov 21 09:22:49 2016 -0500 |
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| @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR under_represented_FDR |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/input.matrix.wt_GSNO_vs_wt_ph8.DESeq2.DE_results.P0.001_C2.wt_ph8-UP.subset.GOseq.enriched Mon Nov 21 09:22:49 2016 -0500 |
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| @@ -0,0 +1,1 @@ +category over_represented_pvalue under_represented_pvalue numDEInCat numInCat term ontology over_represented_FDR |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/results.matrix --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/results.matrix Mon Nov 21 09:22:49 2016 -0500 |
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| @@ -0,0 +1,14 @@ + wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR24|c0_g1_i1 90.00 67.00 85.00 36.00 35.00 34.00 222.00 196.00 201.00 +TR4277|c0_g1_i1 4466.00 4701.00 4284.00 118.00 134.00 164.00 172.00 162.00 170.00 +TR2779|c0_g1_i1 186.00 137.00 217.00 147.00 186.00 197.00 1088.00 1094.00 1086.00 +TR2672|c0_g1_i1 14.00 29.00 22.00 0.00 4.00 2.00 14.00 4.00 7.00 +TR127|c1_g1_i1 9.00 23.00 16.00 2.00 0.00 1.00 3.00 1.00 1.00 +TR2107|c1_g1_i1 59.00 65.00 47.00 6.00 6.00 7.00 3.00 1.00 2.00 +TR5055|c0_g2_i1 36.00 17.00 27.00 4.00 7.00 3.00 4.00 4.00 11.00 +TR3091|c0_g1_i1 22.00 17.00 19.00 250.00 308.00 284.00 333.00 343.00 316.00 +TR4761|c0_g1_i1 2089.00 1746.00 1875.00 155.00 174.00 165.00 394.00 389.00 406.00 +TR131|c0_g1_i1 32.00 28.00 31.00 1001.00 1233.00 1208.00 1486.00 1492.00 1457.00 +TR5075|c0_g1_i1 13.00 22.00 21.00 6.00 8.00 10.00 163.00 121.00 142.00 +TR1894|c2_g1_i1 21.00 14.00 11.00 1.00 2.00 5.00 1.00 3.00 1.00 +TR3788|c0_g1_i1 17.00 30.00 22.00 91.00 132.00 125.00 32.00 22.00 27.00 |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/results.matrix.RData |
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| @@ -0,0 +1,14 @@ +wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR24|c0_g1_i1 0.106533882165825 -0.313797916782532 0.025003996669227 -1.19180739240392 -1.23133575659056 -1.2719777410879 1.39963914188743 1.22079106142351 1.25695072471892 +TR4277|c0_g1_i1 3.24415794782388 3.31812623217364 3.18414689752048 -1.98611482817144 -1.80411699442855 -1.51461037723356 -1.44630436384266 -1.5322044372483 -1.46308007659348 +TR2779|c0_g1_i1 -0.795433018475884 -1.23380302158535 -0.574143153586594 -1.13287411273457 -0.795433018475884 -0.712970858283911 1.74646076035339 1.75438767612502 1.74380874666379 +TR2672|c0_g1_i1 0.965440325233136 1.96544032523314 1.58211168568163 -2.94145027037538 -0.619522175488021 -1.35648776965423 0.965440325233136 -0.619522175488021 0.0585497296246169 +TR127|c1_g1_i1 1.25755965737847 2.52059406321227 2.02309440374145 -0.479405936787734 -2.06436843750889 -1.06436843750889 -0.0643684375088904 -1.06436843750889 -1.06436843750889 +TR2107|c1_g1_i1 2.49178842221691 2.62929194596684 2.16986032732955 -0.607747251334006 -0.607747251334006 -0.41510217339161 -1.41510217339161 -2.41510217339161 -1.83013967267045 +TR5055|c0_g2_i1 1.90528891290538 0.865760548718745 1.50319046933404 -0.982236357836205 -0.304164452723568 -1.30416445272357 -0.982236357836205 -0.982236357836205 0.280798047997588 +TR3091|c0_g1_i1 -2.42438780178849 -2.77802475640319 -2.62602166295814 1.02359379610527 1.32351327005887 1.20686835120661 1.43575453462855 1.4783149968566 1.36038927229391 +TR4761|c0_g1_i1 2.06406810079911 1.80544476674762 1.90822498634624 -1.67981690730689 -1.51400801433681 -1.59017969482221 -0.339510283104669 -0.357888812419525 -0.296334141902888 +TR131|c0_g1_i1 -3.50802026981862 -3.6944333940495 -3.55241438917708 1.41625240401813 1.71671228997234 1.68718414007205 1.98577454287534 1.99158406095747 1.95736061514986 +TR5075|c0_g1_i1 -1.04544737992556 -0.329240345926152 -0.393370683345868 -2.04544737992556 -1.68287730054085 -1.39337068334587 2.50474970263492 2.07793503557972 2.30706903479522 +TR1894|c2_g1_i1 2.11263053903627 1.56008951600749 1.23816142112012 -1.34680107960103 -0.761838578879876 0.238161421120124 -1.34680107960103 -0.346801079601032 -1.34680107960103 +TR3788|c0_g1_i1 -1.22775484082629 -0.443483531881724 -0.874117886211586 1.12588211378841 1.65760259323259 1.57960008123132 -0.353285722910146 -0.874117886211586 -0.590324920210995 |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/analyze_diff_expr/results.matrix.log2.dat --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/analyze_diff_expr/results.matrix.log2.dat Mon Nov 21 09:22:49 2016 -0500 |
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| @@ -0,0 +1,14 @@ +wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +TR24|c0_g1_i1 6.5077946401987 6.08746284125034 6.4262647547021 5.20945336562895 5.16992500144231 5.12928301694497 7.8008998999203 7.62205181945638 7.65821148275179 +TR4277|c0_g1_i1 12.1250905393033 12.199058823653 12.0650794889999 6.89481776330794 7.07681559705083 7.36632221424582 7.43462822763672 7.34872815423108 7.4178525148859 +TR2779|c0_g1_i1 7.54689445988764 7.10852445677817 7.76818432477693 7.20945336562895 7.54689445988764 7.62935662007961 10.0887882387169 10.0967151544885 10.0861362250273 +TR2672|c0_g1_i1 3.90689059560852 4.90689059560852 4.52356195605701 0 2.32192809488736 1.58496250072116 3.90689059560852 2.32192809488736 3 +TR127|c1_g1_i1 3.32192809488736 4.58496250072116 4.08746284125034 1.58496250072116 0 1 2 1 1 +TR2107|c1_g1_i1 5.90689059560852 6.04439411935845 5.58496250072116 2.8073549220576 2.8073549220576 3 2 1 1.58496250072116 +TR5055|c0_g2_i1 5.20945336562895 4.16992500144231 4.8073549220576 2.32192809488736 3 2 2.32192809488736 2.32192809488736 3.58496250072116 +TR3091|c0_g1_i1 4.52356195605701 4.16992500144231 4.32192809488736 7.97154355395077 8.27146302790437 8.1548181090521 8.38370429247405 8.4262647547021 8.30833903013941 +TR4761|c0_g1_i1 11.0292872269682 10.7706638929168 10.8734441125154 7.28540221886225 7.45121111183233 7.37503943134692 8.62570884306447 8.60733031374961 8.66888498426625 +TR131|c0_g1_i1 5.04439411935845 4.85798099512757 5 9.96866679319521 10.2691266791494 10.2395985292491 10.5381889320524 10.5439984501345 10.5097750043269 +TR5075|c0_g1_i1 3.8073549220576 4.52356195605701 4.4594316186373 2.8073549220576 3.16992500144231 3.4594316186373 7.35755200461808 6.93073733756289 7.15987133677839 +TR1894|c2_g1_i1 4.4594316186373 3.90689059560852 3.58496250072116 1 1.58496250072116 2.58496250072116 1 2 1 +TR3788|c0_g1_i1 4.16992500144231 4.95419631038687 4.52356195605701 6.52356195605701 7.05528243550119 6.97727992349992 5.04439411935845 4.52356195605701 4.8073549220576 |
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| @@ -0,0 +1,10 @@ +wt_37_2 wt_37_3 wt_37_1 wt_GSNO_3 wt_GSNO_1 wt_GSNO_2 wt_ph8_3 wt_ph8_1 wt_ph8_2 +wt_37_2 1 0.968650822800566 0.985499030254524 0.457364683078012 0.443497697874748 0.451451348748615 0.41961787977306 0.444203836374748 0.448348619980356 +wt_37_3 0.968650822800566 1 0.98879028662025 0.400031307625771 0.378330685571456 0.396636302989378 0.39057945325073 0.383299487197462 0.388022080096891 +wt_37_1 0.985499030254524 0.98879028662025 1 0.452638132682111 0.434834315692609 0.44176483058741 0.461437515072935 0.462172448553839 0.473652431554024 +wt_GSNO_3 0.457364683078012 0.400031307625771 0.452638132682111 1 0.965144031362199 0.979742518682039 0.844139129634192 0.862862111399854 0.857171072391268 +wt_GSNO_1 0.443497697874748 0.378330685571456 0.434834315692609 0.965144031362199 1 0.983818328020852 0.858668155107621 0.871693931267863 0.876908826664397 +wt_GSNO_2 0.451451348748615 0.396636302989378 0.44176483058741 0.979742518682039 0.983818328020852 1 0.854388461031158 0.878292745544781 0.861156659158544 +wt_ph8_3 0.41961787977306 0.39057945325073 0.461437515072935 0.844139129634192 0.858668155107621 0.854388461031158 1 0.984071267766826 0.98764423106737 +wt_ph8_1 0.444203836374748 0.383299487197462 0.462172448553839 0.862862111399854 0.871693931267863 0.878292745544781 0.984071267766826 1 0.989191009161984 +wt_ph8_2 0.448348619980356 0.388022080096891 0.473652431554024 0.857171072391268 0.876908826664397 0.861156659158544 0.98764423106737 0.989191009161984 1 |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/trinotate/genes.lengths.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/trinotate/genes.lengths.txt Mon Nov 21 09:22:49 2016 -0500 |
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| @@ -0,0 +1,40 @@ +gene_id length +TR24|c0_g1_i1 290.00 +TR2779|c0_g1_i1 186.00 +TR127|c1_g1_i1 229.00 +TR2107|c1_g1_i1 259.00 +TR2011|c5_g1_i1 211.00 +TR4163|c0_g1_i1 368.00 +TR5055|c0_g2_i1 236.00 +TR1449|c0_g1_i1 196.00 +TR1982|c2_g1_i1 227.00 +TR1859|c3_g1_i1 220.00 +TR1492|c0_g1_i2 195.00 +TR1122|c0_g1_i1 222.00 +TR2278|c0_g1_i1 497.00 +TR4084|c0_g1_i1 295.00 +TR4761|c0_g1_i1 289.00 +TR3638|c0_g1_i1 247.00 +TR2090|c0_g1_i1 220.00 +TR3854|c0_g1_i1 178.00 +TR131|c0_g1_i1 232.00 +TR5075|c0_g1_i1 213.00 +TR2182|c3_g2_i6 221.44 +TR3788|c0_g1_i1 217.00 +TR4859|c0_g1_i1 226.00 +TR2487|c0_g1_i1 386.00 +TR2122|c0_g2_i2 145.00 +TR4277|c0_g1_i1 466.00 +TR3091|c0_g1_i1 222.00 +TR2130|c1_g3_i1 220.00 +TR3807|c0_g1_i1 226.00 +TR1894|c2_g1_i1 221.00 +TR5212|c0_g1_i1 264.00 +TR939|c0_g1_i1 296.00 +TR1891|c0_g1_i1 115.00 +TR2672|c0_g1_i1 214.00 +TR2844|c0_g1_i1 166.00 +TR1837|c2_g1_i1 221.00 +TR1678|c0_g1_i1 221.00 +TR3249|c0_g1_i1 221.00 +TR1479|c0_g1_i1 136.00 |
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| diff -r 405e436ec8b3 -r 2d2e0769164c test-data/count/trinotate/go_annotations.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/count/trinotate/go_annotations.txt Mon Nov 21 09:22:49 2016 -0500 |
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| b'@@ -0,0 +1,39 @@\n+TR24|c0_g1_i1\tGO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360\n+TR2779|c0_g1_i1\tGO:0003674,GO:0003824,GO:0004596,GO:0005575,GO:0005634,GO:0005737,GO:0008080,GO:0016407,GO:0016410,GO:0016740,GO:0016746,GO:0016747,GO:0034212,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464\n+TR127|c1_g1_i1\tGO:0003674,GO:0003824,GO:0004310,GO:0004311,GO:0004659,GO:0005575,GO:0005789,GO:0006066,GO:0006629,GO:0006694,GO:0006720,GO:0008150,GO:0008152,GO:0008202,GO:0008299,GO:0008610,GO:0009058,GO:0009987,GO:0016020,GO:0016021,GO:0016125,GO:0016126,GO:0016491,GO:0016740,GO:0016765,GO:0031090,GO:0044237,GO:0044238,GO:0044249,GO:0044255,GO:0044281,GO:0044283,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044711,GO:0044763,GO:0046165,GO:0051996,GO:0071704,GO:0098588,GO:0098589,GO:1901360,GO:1901362,GO:1901576,GO:1901615,GO:1901617\n+TR2107|c1_g1_i1\tGO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139,GO:0006259,GO:0006310,GO:0006725,GO:0006807,GO:0008150,GO:0008152,GO:0008233,GO:0009987,GO:0015074,GO:0016740,GO:0016772,GO:0016779,GO:0016787,GO:0016788,GO:0034061,GO:0034641,GO:0043167,GO:0043169,GO:0043170,GO:0044237,GO:0044238,GO:0044260,GO:0046483,GO:0046872,GO:0070001,GO:0070011,GO:0071704,GO:0090304,GO:0097159,GO:1901360,GO:1901363\n+TR2011|c5_g1_i1\tGO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005737,GO:0006801,GO:0006810,GO:0006811,GO:0006812,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169,GO:0044237,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044765,GO:0046872,GO:0046914,GO:0051234,GO:0055114,GO:0072593\n+TR4163|c0_g1_i1\tGO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005634,GO:0005743,GO:0005829,GO:0006801,GO:0006873,GO:0006875,GO:0006878,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0010035,GO:0010038,GO:0016020,GO:0016530,GO:0016531,GO:0016532,GO:0019725,GO:0019866,GO:0030003,GO:0030234,GO:0031090,GO:0031966,GO:0042221,GO:0042592,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044237,GO:0044422,GO:0044424,GO:0044429,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044763,GO:0046872,GO:0046914,GO:0046916,GO:0048878,GO:0050801,GO:0050896,GO:0051716,GO:0055065,GO:0055070,GO:0055076,GO:0055080,GO:0055082,GO:0055114,GO:0065007,GO:0065008,GO:0070887,GO:0071241,GO:0071248,GO:0072593\n+TR5055|c0_g2_i1\tGO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872,GO:0046914\n+TR1449|c0_g1_i1\tGO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872,GO:0046914\n+TR1982|c2_g1_i1\tGO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360\n+TR1859|c3_g1_i1\tGO:0003676\n+TR1492|c0_g1_i2\tGO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229\n+TR1122|c0_g1_i1\tGO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234\n+TR2278|c0_g1_i1\tGO:0031090,GO:0033765\n+TR4084|c0_g1_i1\tGO:0003674,GO:0005488,GO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043'..b'89,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360\n+TR131|c0_g1_i1\tGO:0031090,GO:0033765\n+TR5075|c0_g1_i1\tGO:0031090,GO:0033765\n+TR2182|c3_g2_i6\tGO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139\n+TR3788|c0_g1_i1\tGO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229\n+TR4859|c0_g1_i1\tGO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139\n+TR2487|c0_g1_i1\tGO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169\n+TR2122|c0_g2_i2\tGO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872\n+TR4277|c0_g1_i1\tGO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872\n+TR3091|c0_g1_i1\tGO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169\n+TR2130|c1_g3_i1\tGO:0003674,GO:0003824,GO:0003865,GO:0005575,GO:0005783,GO:0005789,GO:0006629,GO:0008150,GO:0008152,GO:0008202,GO:0016020,GO:0016021,GO:0016229,GO:0016491,GO:0016627,GO:0031090,GO:0033765,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044238,GO:0044422,GO:0044424,GO:0044425,GO:0044432,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0071704,GO:0098588,GO:0098589,GO:1901360\n+TR3807|c0_g1_i1\tGO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005634,GO:0005743,GO:0005829,GO:0006801,GO:0006873,GO:0006875,GO:0006878,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0010035,GO:0010038,GO:0016020,GO:0016530,GO:0016531,GO:0016532,GO:0019725,GO:0019866,GO:0030003,GO:0030234,GO:0031090,GO:0031966,GO:0042221,GO:0042592,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044237,GO:0044422,GO:0044424,GO:0044429,GO:0044444,GO:0044446,GO:0044464,GO:0044699,GO:0044710,GO:0044763,GO:0046872,GO:0046914,GO:0046916,GO:0048878,GO:0050801,GO:0050896,GO:0051716,GO:0055065,GO:0055070,GO:0055076,GO:0055080,GO:0055082,GO:0055114,GO:0065007,GO:0065008,GO:0070887,GO:0071241,GO:0071248,GO:0072593\n+TR1894|c2_g1_i1\tGO:0005575,GO:0005634,GO:0008270,GO:0043167,GO:0043169,GO:0043226,GO:0043227,GO:0043229,GO:0043231,GO:0044424,GO:0044464,GO:0046872\n+TR5212|c0_g1_i1\tGO:0003865,GO:0005575,GO:0005783\n+TR939|c0_g1_i1\tGO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175,GO:0004190,GO:0004518,GO:0004519,GO:0005488,GO:0006139\n+TR1891|c0_g1_i1\tGO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175\n+TR2672|c0_g1_i1\tGO:0003865,GO:0005575,GO:0005783\n+TR2844|c0_g1_i1\tGO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234\n+TR1837|c2_g1_i1\tGO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005737,GO:0006801,GO:0006810,GO:0006811,GO:0006812,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169,GO:0044237,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044765,GO:0046872,GO:0046914,GO:0051234,GO:0055114,GO:0072593\n+TR1678|c0_g1_i1\tGO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175\n+TR3249|c0_g1_i1\tGO:0003674,GO:0003676,GO:0003677,GO:0003723,GO:0003824,GO:0003887,GO:0003964,GO:0004175\n+TR1479|c0_g1_i1\tGO:0003674,GO:0005488,GO:0005507,GO:0005575,GO:0005737,GO:0006801,GO:0006810,GO:0006811,GO:0006812,GO:0008047,GO:0008150,GO:0008152,GO:0009987,GO:0016530,GO:0016531,GO:0016532,GO:0030001,GO:0030234,GO:0043167,GO:0043169,GO:0044237,GO:0044424,GO:0044464,GO:0044699,GO:0044710,GO:0044765,GO:0046872,GO:0046914,GO:0051234,GO:0055114,GO:0072593\n' 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