Mercurial > repos > yhoogstrate > edger_with_design_matrix
changeset 8:31a23ae7c61e draft default tip
planemo upload for repository https://github.com/ErasmusMC-Bioinformatics/galaxytools-emc/tree/master/tools/edger_with_design_matrix commit eb5cd7834861d8ddbffce974ed0ca6f1c0ecccf2
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--- a/edgeR_Concatenate_Expression_Matrices.xml Wed Feb 08 10:28:17 2017 -0500 +++ b/edgeR_Concatenate_Expression_Matrices.xml Tue Feb 14 10:01:51 2017 -0500 @@ -95,8 +95,10 @@ </when> </conditional> - <param name="remove_comment_lines" type="boolean" label="Automatically remove 'comment' lines starting with a '#'" truevale="true" falsevalue="false" selected="true" help="Some tools (incl. featureCounts) include comment lines that are not neccesairy for downstream analyis. By enabling this function, these lines will be removed." /> - + <param name="remove_comment_lines" type="boolean" truevalue="true" falsevalue="false" checked="true" + label="Automatically remove 'comment' lines starting with a '#'" + help="Some tools (incl. featureCounts) include comment lines that are not neccesairy for downstream analyis. By enabling this function, these lines will be removed." /> + </inputs> <outputs>
--- a/edgeR_Convert_DGE_Table_to_Bedgraph.xml Wed Feb 08 10:28:17 2017 -0500 +++ b/edgeR_Convert_DGE_Table_to_Bedgraph.xml Tue Feb 14 10:01:51 2017 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0" encoding="UTF-8"?> - <tool id="edger_dge_table_to_bedgraph" name="edgeR: Convert 'differentially expressed genes'-table to bedgraph(s)" version="1.0.0.b"> + <tool id="edger_dge_table_to_bedgraph" name="edgeR: Convert 'differentially expressed genes'-table to bedgraph(s)" version="1.0.0.c"> <description>EdgeR's "differentially expressed genes" table to bedgraph(s)</description> <macros> @@ -7,11 +7,11 @@ </macros> <requirements> - <requirement type="package" version="1.0.0">edger_dge_table_to_bedgraph</requirement> + <requirement type="package" version="2.7">python</requirement> </requirements> <command> - edger_dge_table_to_bedgraph + python '${__tool_directory__}/bin/edger_dge_table_to_bedgraph' -t $cpm_table -g $geneset
--- a/edgeR_Design_from_Expression_Matrix.xml Wed Feb 08 10:28:17 2017 -0500 +++ b/edgeR_Design_from_Expression_Matrix.xml Tue Feb 14 10:01:51 2017 -0500 @@ -7,11 +7,11 @@ </macros> <requirements> - <requirement type="package" version="1.0.0">design_matrix_creator</requirement> + <requirement type="package" version="2.7">python</requirement> </requirements> <command> - design_matrix_creator + python '${__tool_directory__}/bin/design_matrix_creator' -c $expression_matrix #set $unique_columns = [] @@ -57,7 +57,7 @@ </command> <inputs> - <param format="tabular" name="expression_matrix" type="data" label="Expression matrix (read counts)" help="You can create a count matrix with the tool" /> + <param name="expression_matrix" format="tabular" type="data" label="Expression matrix (read counts)" help="You can create a count matrix with the tool" /> <repeat name="treatments" title="Factor/Condition" min="1"> <param name="name" type="text" value="FactorName" label="Specify a name for the factor / condition" help="e.g. 'Tumor vs. Normal', 'Timepoint' or 'DiseaseState'. Field must be non-numerical, preferably only letters!!" /> @@ -96,20 +96,19 @@ <test> <param name="expression_matrix" value="GSE51403/GSE51403_expression_matrix_full.txt" /> - <!-- <repeat name="treatments"> --> - <param name="treatments_0|name" value="Treatment" /> - <!-- <repeat name="rep_factorLevel"> --> - <param name="treatments_0|rep_factorLevel_0|factorLevel" value="Control" /> - <param name="treatments_0|rep_factorLevel_0|factorIndex" value="2,3,4,5,6,7,8" /> - <!-- </repeat> --> - <!-- <repeat name="rep_factorLevel"> --> - <param name="treatments_0|rep_factorLevel_1|factorLevel" value="E2" /> - <param name="treatments_0|rep_factorLevel_1|factorIndex" value="9,10,11,12,13,14,15" /> - <!-- </repeat> --> - <!-- </repeat> --> + <repeat name="treatments"> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="Control" /> + <param name="factorIndex" value="2,3,4,5,6,7,8" /> + </repeat> + <repeat name="rep_factorLevel"> + <param name="factorLevel" value="E2" /> + <param name="factorIndex" value="9,10,11,12,13,14,15" /> + </repeat> + </repeat> <conditional name="choose_blocking"> - <param value="false" /> + <param name="choice" value="false" /> </conditional> <output name="design_matrix" file="GSE51403/GSE51403_design_matrix_full_depth.txt" />
--- a/edgeR_Differential_Gene_Expression.xml Wed Feb 08 10:28:17 2017 -0500 +++ b/edgeR_Differential_Gene_Expression.xml Tue Feb 14 10:01:51 2017 -0500 @@ -7,7 +7,7 @@ </macros> <requirements> - <requirement type="package" version="3.11.0">edger</requirement> + <requirement type="package" version="3.12.1">bioconductor-edger</requirement> </requirements> <stdio>
--- a/edgeR_macros.xml Wed Feb 08 10:28:17 2017 -0500 +++ b/edgeR_macros.xml Tue Feb 14 10:01:51 2017 -0500 @@ -3,17 +3,7 @@ ------- The tool wrapper has been written by Youri Hoogstrate from the Erasmus -Medical Center (Rotterdam, Netherlands) on behalf of the Translational -Research IT (TraIT) project: - -http://www.ctmm.nl/en/programmas/infrastructuren/traitprojecttranslationeleresearch - -More tools by the Translational Research IT (TraIT) project can be found -in the following toolsheds: - -http://toolshed.g2.bx.psu.edu - -http://testtoolshed.g2.bx.psu.edu/ +Medical Center (Rotterdam, Netherlands) I would like to thank Hina Riaz - Naz Khan for her helpful contribution.</token>
--- a/test-data/Differential_Gene_Expression/differentially_expressed_genes.batch-effects.tabular.txt Wed Feb 08 10:28:17 2017 -0500 +++ b/test-data/Differential_Gene_Expression/differentially_expressed_genes.batch-effects.tabular.txt Tue Feb 14 10:01:51 2017 -0500 @@ -1,29 +1,29 @@ "" "genes" "logFC" "logCPM" "LR" "PValue" "FDR" -"15" "RET" 1.95351498277649 13.2940435307943 70.7884298827703 3.9766237329402e-17 1.15322088255266e-15 -"24" "HSPA8" 0.607097086193171 18.9380827005326 18.3388522248215 1.84897696413517e-05 0.000268101659799599 -"12" "IFI44L" -0.663271215486821 11.7020333673755 10.9083408215917 0.00095732231526494 0.00925411571422775 -"10" "MYO18A" -0.607030110998538 14.1586814058554 8.85972925087567 0.0029153081194653 0.0208760330354099 -"4" "DDX11" 0.724160415576466 12.4597575302041 8.47565074268945 0.00359931604058791 0.0208760330354099 -"26" "NR2C2AP" 0.538450796715875 12.9331552590697 6.96854404518889 0.00829549660040106 0.0400949002352718 -"19" "RASSF3" -0.323616221214522 12.4964626371138 3.7019217136962 0.05434983717189 0.225163611140687 -"3" "DDX17" -0.20201533346913 16.1804174471336 2.4240349611365 0.119486805704499 0.43313967067881 -"2" "USP26" -2.19888949506255 4.27316802151059 2.23930233943077 0.1345416719394 0.433523165138066 -"27" "INADL" -0.171504044976009 15.2186072712825 1.49672630947915 0.221175760548511 0.641409705590681 -"21" "LYSMD3" -0.194806526906794 13.32535006408 1.33073961519612 0.248673682102714 0.655594252816247 -"16" "IQCG" -0.208260226810614 10.1622224199572 0.967867000668835 0.3252127194599 0.785930738694759 -"6" "SLC35D3" 0.789817686242913 4.62274850327991 0.638997348362095 0.424074105189856 0.922823270583707 -"14" "KCNAB3" 0.224776816841962 7.85434240586327 0.477050454902194 0.489761385678098 0.922823270583707 -"20" "FUT8" -0.100266057923686 15.3006920075591 0.448528599960923 0.503034528215111 0.922823270583707 -"1" "COMMD10" 0.129868119349192 12.8850203875481 0.43582621570193 0.509143873425494 0.922823270583707 -"9" "TXLNB" -0.183590716507963 7.2825391341052 0.269612199658876 0.603592030691037 0.990834288521076 -"28" "TMEM31" -0.231195333650393 6.16897757110336 0.252957033365721 0.615000592875151 0.990834288521076 -"17" "C20orf118" 0.163495741844413 6.73904801103973 0.171566008065263 0.678723780532467 1 -"7" "GLOD4" -0.0679141042839315 13.8710260882794 0.154827011727691 0.693964522467115 1 -"22" "LMOD3" 0.0791372844747401 7.60390982671528 0.0540610465986004 0.816141676483626 1 -"8" "GIMAP7" 0.195152071961945 4.26623062002702 0.0194047958154413 0.889212222514442 1 -"23" "HIPK1" -0.00677640818725696 17.7957744498389 0.00305975315578166 0.955887483884316 1 -"11" "ATG4B" 0.00473988666702576 13.5252482941211 0.000418258796557325 0.983683299966982 1 -"13" "KHSRP" -0.00184247000571017 14.7206397592923 0.000136964665301775 0.990662418229392 1 +"15" "RET" 1.95351498277648 13.2940435307943 70.7884298825789 3.97662373332596e-17 1.15322088266453e-15 +"24" "HSPA8" 0.60709708619317 18.9380827005326 18.338852224771 1.84897696418416e-05 0.000268101659806703 +"12" "IFI44L" -0.663271215486821 11.7020333673755 10.9083408215897 0.00095732231526599 0.0092541157142379 +"10" "MYO18A" -0.607030110998537 14.1586814058554 8.85972925085778 0.00291530811949387 0.0208760330353944 +"4" "DDX11" 0.724160415576466 12.4597575302041 8.4756507426908 0.00359931604058523 0.0208760330353944 +"26" "NR2C2AP" 0.538450796715876 12.9331552590697 6.96854404519358 0.0082954966003793 0.0400949002351666 +"19" "RASSF3" -0.323616221214522 12.4964626371138 3.70192171369743 0.0543498371718503 0.225163611140523 +"3" "DDX17" -0.20201533346913 16.1804174471336 2.42403496111984 0.11948680570577 0.433139670683417 +"2" "USP26" -2.19888949506256 4.27316802151059 2.23930233943077 0.1345416719394 0.433523165138066 +"27" "INADL" -0.171504044976007 15.2186072712825 1.49672630947888 0.221175760548553 0.641409705590803 +"21" "LYSMD3" -0.194806526906797 13.32535006408 1.33073961519338 0.248673682103202 0.655594252817531 +"16" "IQCG" -0.208260226810613 10.1622224199572 0.967867000668792 0.325212719459911 0.785930738694785 +"6" "SLC35D3" 0.789817686242913 4.62274850327991 0.638997348362098 0.424074105189855 0.922823270583379 +"14" "KCNAB3" 0.224776816841962 7.85434240586327 0.477050454902207 0.489761385678092 0.922823270583379 +"20" "FUT8" -0.100266057923687 15.3006920075591 0.448528599955097 0.503034528217885 0.922823270583379 +"1" "COMMD10" 0.129868119349192 12.8850203875481 0.435826215702303 0.509143873425312 0.922823270583379 +"9" "TXLNB" -0.183590716507963 7.2825391341052 0.269612199658886 0.60359203069103 0.990834288521017 +"28" "TMEM31" -0.231195333650393 6.16897757110336 0.252957033365774 0.615000592875114 0.990834288521017 +"17" "C20orf118" 0.163495741844411 6.73904801103973 0.171566008065274 0.678723780532458 1 +"7" "GLOD4" -0.0679141042839328 13.8710260882794 0.154827011726031 0.693964522468672 1 +"22" "LMOD3" 0.0791372844747401 7.60390982671528 0.0540610465986839 0.816141676483487 1 +"8" "GIMAP7" 0.195152071961945 4.26623062002702 0.0194047958154386 0.88921222251445 1 +"23" "HIPK1" -0.00677640818725792 17.7957744498389 0.00305975312272722 0.955887484122347 1 +"11" "ATG4B" 0.00473988666702704 13.5252482941211 0.000418258797196813 0.98368329995451 1 +"13" "KHSRP" -0.00184247000570504 14.7206397592923 0.000136964663354888 0.990662418295754 1 "5" "PTPN20B" 0 4.09631395702755 0 1 1 "18" "GPIHBP1" 0 4.09631395702755 0 1 1 "25" "TAS2R39" 0 4.09631395702755 0 1 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/FDR.output.bedgraph Tue Feb 14 10:01:51 2017 -0500 @@ -0,0 +1,10 @@ +chr1 1000 1100 0.99 +chr1 2000 2100 0.98 +chr2 1000 1100 0.94 +chr2 2000 2100 0.93 +chr3 1000 1100 0.86 +chr3 2000 2100 0.65 +chrMt 1000 1100 0.34 +chrMt 2000 2100 0.19 +chrX 1000 1100 0.62 +chrX 2000 2100 0.62
--- a/test-data/GSE51403/GSE51403_design_matrix_full_depth.txt Wed Feb 08 10:28:17 2017 -0500 +++ b/test-data/GSE51403/GSE51403_design_matrix_full_depth.txt Tue Feb 14 10:01:51 2017 -0500 @@ -1,4 +1,4 @@ -sample-name Treatment +sample-name FactorName GSM1244816: Control_Rep1 Control GSM1244817: Control_Rep2 Control GSM1244818: Control_Rep3 Control
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSE51403_design_matrix_full_depth.txt Tue Feb 14 10:01:51 2017 -0500 @@ -0,0 +1,15 @@ +sample-name FactorName +GSM1244816: Control_Rep1 Control +GSM1244817: Control_Rep2 Control +GSM1244818: Control_Rep3 Control +GSM1244819: Control_Rep4 Control +GSM1244820: Control_Rep5 Control +GSM1244821: Control_Rep6 Control +GSM1244822: Control_Rep7 Control +GSM1244809: E2_Rep1 E2 +GSM1244810: E2_Rep2 E2 +GSM1244811: E2_Rep3 E2 +GSM1244812: E2_Rep4 E2 +GSM1244813: E2_Rep5 E2 +GSM1244814: E2_Rep6 E2 +GSM1244815: E2_Rep7 E2
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSE51403_expression_matrix_Control_1.txt Tue Feb 14 10:01:51 2017 -0500 @@ -0,0 +1,22142 @@ +Geneid GSM1244816: Control_Rep1 +COMMD10 966 +USP26 1 +DDX17 8544 +DDX11 329 +PTPN20B 0 +SLC35D3 1 +GLOD4 1614 +GIMAP7 0 +TXLNB 15 +MYO18A 1775 +ATG4B 936 +IFI44L 347 +KHSRP 2557 +KCNAB3 20 +RET 331 +IQCG 125 +C20orf118 9 +GPIHBP1 0 +RASSF3 658 +FUT8 4834 +LYSMD3 1333 +LMOD3 12 +HIPK1 24218 +HSPA8 44244 +TAS2R39 0 +NR2C2AP 606 +INADL 4315 +TMEM31 5 +GC 0 +SPP1 0 +ATP6V1B1 271 +GBX2 12 +GALR1 0 +NEDD4L 1166 +GALNT4 486 +MBD4 1710 +PEX10 245 +NXF2 0 +MYOZ1 1 +C9orf64 666 +ACSF3 557 +DHX16 1187 +SLC26A11 351 +AP4S1 237 +TM2D2 590 +ABHD11 1591 +DEFB109P1B 0 +BPHL 387 +INTS9 371 +EFCAB5 2 +LOC220594 45 +C6orf52 48 +TMPRSS7 8 +EDEM2 1084 +PDIK1L 797 +CD8A 59 +HLA-J 29 +AMT 19 +UBE2L3 2731 +PMS2L2 0 +FAM159A 0 +FAM58B 0 +PPP1R9A 1235 +ERCC1 678 +C19orf48 1275 +RAB34 6 +SLC4A11 74 +EIF2A 3423 +TAF3 516 +ATAD3B 53 +CDCA8 852 +PPIA 38044 +RBM17 2593 +LOC100130776 73 +CLEC1A 0 +C20orf96 105 +NR4A1 507 +FMO3 0 +LAT2 22 +RBMXL2 0 +EDC4 1575 +PNPLA8 2215 +TACR1 9 +GPR137 425 +COQ7 489 +FBXO32 325 +LYPD6B 1613 +CXCL12 62 +DCLRE1C 604 +NFASC 50 +DNAJC5 1672 +PUS7 1191 +B3GALNT1 764 +FANCD2 1412 +ZNF709 255 +GCNT2 46 +TAF15 2495 +CBY1 566 +C6orf70 522 +CCL17 0 +MATN3 187 +MAN2A1 1935 +ZNF343 198 +POMT2 804 +VPS13B 1582 +KIAA0748 0 +TSPAN33 439 +C20orf141 0 +FAM113A 254 +THUMPD3 2323 +GOLGA2B 343 +LLGL2 1638 +GOLGA4 4431 +RASA1 2169 +RPL36A 22835 +SUGP2 1430 +ARHGAP25 0 +PCBP3 203 +ALPK1 306 +REPS1 1068 +GPR82 36 +KIAA0391 1609 +UBE3C 5073 +ANKRD10 504 +ADAP1 236 +CEP152 485 +KRT14 0 +CD2BP2 3688 +SLC11A2 3376 +MTBP 276 +SDF2L1 174 +ATMIN 6548 +WWC1 2163 +SLC26A1 15 +SESN1 827 +DACT1 1 +C20orf27 428 +LAMB1 5346 +TP73 20 +PASD1 1 +TAS1R1 1 +AGTRAP 216 +IGLON5 1 +MYL9 0 +NEK11 262 +KLK12 0 +GPLD1 39 +LYNX1 2 +RAD51AP2 0 +CCDC18 127 +NRXN3 297 +CLEC12A 0 +SP140L 545 +VKORC1L1 832 +PNLDC1 2 +CLEC10A 0 +CAMK2G 1577 +CD200R1 11 +KLK8 1 +SCP2 2539 +C20orf196 60 +PSMB4 10549 +C11orf58 4578 +RNF112 4 +C11orf73 713 +LHX6 62 +HSPB8 391 +GAPDHS 21 +UBE2D3 5612 +FITM2 118 +STARD5 88 +CMIP 1319 +PIGY 1615 +SYCN 0 +LILRA5 4 +PPP2R2C 2257 +PSG6 0 +AOX1 48 +SPECC1L 1692 +DUSP13 4 +ACP6 782 +KLK11 10 +PLK4 692 +RAB11FIP1 1991 +TARS2 2113 +ATRN 1449 +DEFA1B 0 +LOC645166 43 +KRT71 0 +CYS1 28 +CTSA 4540 +GATA2 511 +GRRP1 0 +GFOD1 39 +TSPAN8 0 +FLRT3 1369 +KCTD2 1139 +NRBP1 5843 +RWDD2B 1009 +EFEMP2 4 +TRPV6 7 +ATP2A1 31 +DCTN3 778 +DCAF10 1462 +OTOR 1 +LGSN 6 +ASAP3 669 +PCID2 671 +PCDHGB4 2 +C8orf85 48 +RPLP0 55061 +LSM14A 4421 +WDR24 241 +CD79B 0 +RPL10 35960 +CDK16 2508 +C20orf72 1144 +SERPINI1 12 +PPARA 563 +ARL17B 2 +TBCEL 542 +FMR1NB 0 +TTC39B 239 +C9orf98 78 +LOC338739 9 +C20orf79 0 +RNF5P1 1 +ROR2 2 +ZFAND1 1522 +GABARAPL3 1 +GALNTL5 0 +PLA2G4F 144 +SHISA4 151 +BFAR 3426 +PEX5L 3 +TSPAN12 27 +CTLA4 0 +PVRL4 894 +C9orf131 1 +RNF170 663 +ANAPC2 565 +GTF3C1 2429 +ENPEP 315 +NFATC3 1280 +JOSD2 33 +CASP9 162 +STON2 216 +TRIM5 271 +ACRV1 11 +C1QBP 1980 +H2AFX 881 +CSRP3 0 +BAT4 292 +HYAL1 3 +CCL14 0 +PCDH10 11 +LAIR2 0 +IL22RA1 4 +ANTXR1 1005 +SYN1 4 +SPACA4 0 +DPP8 1316 +CDK11B 292 +C3orf39 150 +EPB41L1 2439 +MED4 1027 +C1orf105 0 +HOPX 3 +CDK3 76 +LIMS1 1133 +FAM184A 80 +SLC39A10 938 +ARMCX6 1290 +CST8 0 +FFAR2 77 +GPR22 0 +MANEA 434 +MAPK9 3498 +ST3GAL5 191 +ACTR1A 2148 +TLX1 4 +CLEC5A 0 +CHMP2A 1328 +SNAR-D 0 +SNAR-A14 0 +ADRB2 0 +FTL 25301 +2-Mar 187 +OR56B1 0 +UGGT2 379 +PRKCA 834 +HHEX 127 +MED13 11267 +SHMT2 3325 +CAPN3 5 +RAB39B 185 +INO80C 147 +PVR 465 +ZBTB47 50 +GGT6 93 +MYOZ3 13 +GIGYF2 3042 +FOXN3 2125 +LOC731275 259 +CCL1 0 +SCTR 1 +ARPC3 7469 +ITGA8 0 +PRAMEF14 0 +MSH5 135 +AAGAB 2554 +C20orf144 1 +CAMSAP1L1 3567 +ZNF341 77 +CNTNAP2 17 +CNST 771 +WDR13 484 +NFX1 1735 +ZFP41 290 +SH3D20 1 +C6orf182 173 +PSMD5 2568 +CXCR4 263 +DGUOK 902 +MYO1D 2103 +WDR11 1346 +PCDHB7 57 +RNASEN 2389 +AHCYL2 1230 +CSPG5 17 +DCTN6 572 +CGREF1 536 +ALDH8A1 7 +PGM2L1 621 +FAS 269 +TSC2 1458 +CAMK1 143 +CUL1 2410 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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/GSE51403_expression_matrix_full.txt Tue Feb 14 10:01:51 2017 -0500 @@ -0,0 +1,22142 @@ +Geneid GSM1244816: Control_Rep1 GSM1244817: Control_Rep2 GSM1244818: Control_Rep3 GSM1244819: Control_Rep4 GSM1244820: Control_Rep5 GSM1244821: Control_Rep6 GSM1244822: Control_Rep7 GSM1244809: E2_Rep1 GSM1244810: E2_Rep2 GSM1244811: E2_Rep3 GSM1244812: E2_Rep4 GSM1244813: E2_Rep5 GSM1244814: E2_Rep6 GSM1244815: E2_Rep7 Length +COMMD10 966 1067 438 1231 580 1120 1822 964 812 528 860 863 1044 1146 1424 +USP26 1 0 1 0 1 1 1 0 0 0 0 0 0 0 2794 +DDX17 8544 13335 4579 16358 5286 12513 20547 6995 8079 5994 6596 7939 7924 9026 5211 +DDX11 329 970 221 867 253 673 970 916 632 706 518 903 640 772 3927 +PTPN20B 0 0 0 0 0 0 0 0 0 0 0 0 0 0 6182 +SLC35D3 1 0 0 2 0 0 2 1 0 2 1 0 0 1 2358 +GLOD4 1614 2596 965 2912 1117 2502 4273 1807 1448 1039 1564 1777 1802 2068 1836 +GIMAP7 0 1 0 0 0 0 0 1 0 0 0 0 0 0 1229 +TXLNB 15 29 9 25 19 22 33 14 15 6 17 14 23 23 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213 156 168 1949 +ZNF28 888 1167 465 1438 569 1267 2051 713 810 524 740 777 861 1026 4711 +XPNPEP3 288 486 177 574 193 463 792 257 307 232 293 375 287 371 3057 +SCG2 11 14 7 20 6 12 25 14 6 5 5 7 10 13 2570 +MIR2278 0 0 0 0 0 0 0 0 0 0 0 0 0 0 96 +MIR2277 0 0 0 0 0 0 0 0 0 0 0 0 0 0 93 +MIR2276 0 0 0 0 0 0 0 0 0 0 0 0 0 0 89 +MIR548Q 0 0 0 0 0 0 0 0 0 0 0 0 0 0 82 +MIR2117 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 +MIR2116 2 0 0 0 0 0 1 0 0 3 0 0 0 1 79 +MIR2114 0 0 0 0 0 0 0 0 0 0 0 0 0 0 80 +MIR759 0 0 0 0 0 0 0 0 0 0 0 0 0 0 90 +FEZ1 279 481 143 571 195 445 824 245 188 132 204 266 264 293 3031 +ZBTB39 491 830 313 1067 300 715 1436 486 520 440 464 652 546 689 6237 +BAG5 2449 3287 1405 4008 1477 3319 5711 2414 2582 1775 2377 2743 3010 3219 5254 +TMEM99 406 577 208 737 250 619 1024 351 298 177 315 346 333 410 2166 +RHBDF2 251 759 186 658 230 588 824 563 254 391 259 486 374 450 3604 +TLR10 23 58 15 70 20 41 59 26 41 31 25 32 15 23 3990 +ARL4A 586 791 308 912 374 799 1307 485 435 311 498 462 565 633 3426 +LOC100132715 5 3 1 4 1 5 6 5 5 0 6 2 1 4 1550 +LINS 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2511 +GTPBP3 174 401 114 429 118 294 454 391 285 278 204 354 276 319 2838 +TKT 12187 30128 8085 29129 11006 27372 40096 16383 8119 10629 9817 16991 12782 14827 3063 +TRH 0 0 0 0 0 0 0 0 0 0 2 1 0 0 2007 +LOC100500773 0 0 0 0 0 0 1 1 0 0 0 0 0 0 1362 +ELMOD2 1060 1202 478 1470 652 1299 2116 728 752 511 781 718 948 931 4409 +DCLK2 5 14 4 7 4 7 15 2 4 1 3 6 5 5 4396 +LOC728622 5 14 2 9 4 11 20 5 15 8 7 9 5 4 1882 +MIR1972-1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 152 +ZFHX2 84 232 75 246 59 160 251 79 77 88 54 103 104 83 9181 +C16orf11 0 2 0 0 0 0 0 0 0 0 0 0 0 0 2216 +IFI35 538 1333 415 1286 462 1022 1707 665 356 435 426 602 531 508 1249 +CCDC6 4666 6287 2372 7888 2868 6289 10803 3413 3656 2646 3523 3652 4068 4507 5826 +OR7D2 13 35 13 48 9 29 50 31 11 28 11 20 17 16 3224 +ZNF865 121 355 81 355 96 268 425 153 105 120 105 200 150 177 4949 +RBM5 1539 2792 837 3082 975 2467 3906 1460 1549 1132 1263 1490 1332 1590 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406 5353
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/differentially_expressed_genes.batch-effects.tabular.txt Tue Feb 14 10:01:51 2017 -0500 @@ -0,0 +1,30 @@ +"" "genes" "logFC" "logCPM" "LR" "PValue" "FDR" +"15" "RET" 1.95351498277648 13.2940435307943 70.7884298825789 3.97662373332596e-17 1.15322088266453e-15 +"24" "HSPA8" 0.60709708619317 18.9380827005326 18.338852224771 1.84897696418416e-05 0.000268101659806703 +"12" "IFI44L" -0.663271215486821 11.7020333673755 10.9083408215897 0.00095732231526599 0.0092541157142379 +"10" "MYO18A" -0.607030110998537 14.1586814058554 8.85972925085778 0.00291530811949387 0.0208760330353944 +"4" "DDX11" 0.724160415576466 12.4597575302041 8.4756507426908 0.00359931604058523 0.0208760330353944 +"26" "NR2C2AP" 0.538450796715876 12.9331552590697 6.96854404519358 0.0082954966003793 0.0400949002351666 +"19" "RASSF3" -0.323616221214522 12.4964626371138 3.70192171369743 0.0543498371718503 0.225163611140523 +"3" "DDX17" -0.20201533346913 16.1804174471336 2.42403496111984 0.11948680570577 0.433139670683417 +"2" "USP26" -2.19888949506256 4.27316802151059 2.23930233943077 0.1345416719394 0.433523165138066 +"27" "INADL" -0.171504044976007 15.2186072712825 1.49672630947888 0.221175760548553 0.641409705590803 +"21" "LYSMD3" -0.194806526906797 13.32535006408 1.33073961519338 0.248673682103202 0.655594252817531 +"16" "IQCG" -0.208260226810613 10.1622224199572 0.967867000668792 0.325212719459911 0.785930738694785 +"6" "SLC35D3" 0.789817686242913 4.62274850327991 0.638997348362098 0.424074105189855 0.922823270583379 +"14" "KCNAB3" 0.224776816841962 7.85434240586327 0.477050454902207 0.489761385678092 0.922823270583379 +"20" "FUT8" -0.100266057923687 15.3006920075591 0.448528599955097 0.503034528217885 0.922823270583379 +"1" "COMMD10" 0.129868119349192 12.8850203875481 0.435826215702303 0.509143873425312 0.922823270583379 +"9" "TXLNB" -0.183590716507963 7.2825391341052 0.269612199658886 0.60359203069103 0.990834288521017 +"28" "TMEM31" -0.231195333650393 6.16897757110336 0.252957033365774 0.615000592875114 0.990834288521017 +"17" "C20orf118" 0.163495741844411 6.73904801103973 0.171566008065274 0.678723780532458 1 +"7" "GLOD4" -0.0679141042839328 13.8710260882794 0.154827011726031 0.693964522468672 1 +"22" "LMOD3" 0.0791372844747401 7.60390982671528 0.0540610465986839 0.816141676483487 1 +"8" "GIMAP7" 0.195152071961945 4.26623062002702 0.0194047958154386 0.88921222251445 1 +"23" "HIPK1" -0.00677640818725792 17.7957744498389 0.00305975312272722 0.955887484122347 1 +"11" "ATG4B" 0.00473988666702704 13.5252482941211 0.000418258797196813 0.98368329995451 1 +"13" "KHSRP" -0.00184247000570504 14.7206397592923 0.000136964663354888 0.990662418295754 1 +"5" "PTPN20B" 0 4.09631395702755 0 1 1 +"18" "GPIHBP1" 0 4.09631395702755 0 1 1 +"25" "TAS2R39" 0 4.09631395702755 0 1 1 +"29" "GC" 0 4.09631395702755 0 1 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/differentially_expressed_genes.significant.tabular.txt Tue Feb 14 10:01:51 2017 -0500 @@ -0,0 +1,7 @@ +"" "genes" "logFC" "logCPM" "LR" "PValue" "FDR" +"15" "RET" 1.94897640107286 13.2940435307943 77.6545995415986 1.22730171935022e-18 3.55917498611563e-17 +"24" "HSPA8" 0.607138087178614 18.9380827005326 16.8408380186893 4.06490891119454e-05 0.000589411792123208 +"12" "IFI44L" -0.665544707287881 11.7020333673755 13.7144720195324 0.000212808308075529 0.00205714697806344 +"10" "MYO18A" -0.608389235629078 14.1586814058554 10.0030349277278 0.00156282461006963 0.0113304784230048 +"4" "DDX11" 0.719283453206409 12.4597575302041 9.1203698809081 0.00252778847312638 0.014661173144133 +"26" "NR2C2AP" 0.538719097450497 12.9331552590697 7.88314604309164 0.00498976028708414 0.0241171747209067
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/differentially_expressed_genes.tabular.txt Tue Feb 14 10:01:51 2017 -0500 @@ -0,0 +1,30 @@ +"" "genes" "logFC" "logCPM" "LR" "PValue" "FDR" +"15" "RET" 1.94897640107286 13.2940435307943 77.6545995415986 1.22730171935022e-18 3.55917498611563e-17 +"24" "HSPA8" 0.607138087178614 18.9380827005326 16.8408380186893 4.06490891119454e-05 0.000589411792123208 +"12" "IFI44L" -0.665544707287881 11.7020333673755 13.7144720195324 0.000212808308075529 0.00205714697806344 +"10" "MYO18A" -0.608389235629078 14.1586814058554 10.0030349277278 0.00156282461006963 0.0113304784230048 +"4" "DDX11" 0.719283453206409 12.4597575302041 9.1203698809081 0.00252778847312638 0.014661173144133 +"26" "NR2C2AP" 0.538719097450497 12.9331552590697 7.88314604309164 0.00498976028708414 0.0241171747209067 +"19" "RASSF3" -0.322613484306052 12.4964626371138 4.62652086549247 0.031481339838463 0.130422693616489 +"3" "DDX17" -0.202898462175601 16.1804174471336 2.58563106107022 0.107837421983287 0.390910654689415 +"2" "USP26" -2.18026172235612 4.27316802151059 2.23964990963176 0.134511431832489 0.433425724793576 +"27" "INADL" -0.171517188407228 15.2186072712825 1.67097950803399 0.196127388799313 0.532259040398981 +"21" "LYSMD3" -0.195688416211876 13.32535006408 1.62863926866461 0.201891360151338 0.532259040398981 +"16" "IQCG" -0.204602031239968 10.1622224199572 1.27895197435303 0.258093988887329 0.623727139811046 +"14" "KCNAB3" 0.235558773538239 7.85434240586327 0.626910368891663 0.42849088083079 0.920477060511131 +"6" "SLC35D3" 0.732791849378157 4.62274850327991 0.571073743098566 0.449832554709518 0.920477060511131 +"20" "FUT8" -0.10105286103336 15.3006920075591 0.507763042830561 0.476108824402309 0.920477060511131 +"1" "COMMD10" 0.124183380838807 12.8850203875481 0.427219144492929 0.513356635938278 0.927280503918676 +"9" "TXLNB" -0.182677549934781 7.2825391341052 0.332700920948795 0.564072999466928 0.927280503918676 +"28" "TMEM31" -0.242966946412956 6.16897757110336 0.313478542098543 0.575553416225385 0.927280503918676 +"7" "GLOD4" -0.0680179216917574 13.8710260882794 0.180025725971447 0.671351132982351 0.998117639846733 +"17" "C20orf118" 0.14522927187254 6.73904801103973 0.16086977771818 0.688356992997747 0.998117639846733 +"22" "LMOD3" 0.065379751793664 7.60390982671528 0.0485282385969317 0.825644327619727 1 +"8" "GIMAP7" 0.278076976843342 4.26623062002702 0.0410821671265458 0.839379401017925 1 +"23" "HIPK1" -0.0050354983636938 17.7957744498389 0.00154544012787028 0.968641570606185 1 +"13" "KHSRP" -0.00239769805103114 14.7206397592923 0.000263977502370949 0.987037033096146 1 +"11" "ATG4B" 0.00130641853526229 13.5252482941211 3.5333815787908e-05 0.995257222245289 1 +"5" "PTPN20B" 0 4.09631395702755 0 1 1 +"18" "GPIHBP1" 0 4.09631395702755 0 1 1 +"25" "TAS2R39" 0 4.09631395702755 0 1 1 +"29" "GC" 0 4.09631395702755 0 1 1
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/logFC.output.bedgraph Tue Feb 14 10:01:51 2017 -0500 @@ -0,0 +1,10 @@ +chr1 1000 1100 -1.67 +chr1 2000 2100 3.30 +chr2 1000 1100 2.81 +chr2 2000 2100 2.44 +chr3 1000 1100 -1.49 +chr3 2000 2100 1.74 +chrMt 1000 1100 1.99 +chrMt 2000 2100 -1.29 +chrX 1000 1100 2.36 +chrX 2000 2100 2.01