# HG changeset patch # User yhoogstrate # Date 1400663029 14400 # Node ID 7e45df99a6fc11e5071940285784aa6de7c9efc1 # Parent 87bf067cfc53ce19cb3a67d94325932847c429e8 Uploaded diff -r 87bf067cfc53 -r 7e45df99a6fc design_matrix_creator.py diff -r 87bf067cfc53 -r 7e45df99a6fc edgeR_Differential_Gene_Expression.xml --- a/edgeR_Differential_Gene_Expression.xml Wed May 21 04:55:20 2014 -0400 +++ b/edgeR_Differential_Gene_Expression.xml Wed May 21 05:03:49 2014 -0400 @@ -3,7 +3,7 @@ RNA-Seq gene expression analysis using edgeR (R package) - package_r_3_0_3 + R package_biocLite_edgeR_limma diff -r 87bf067cfc53 -r 7e45df99a6fc test/MCF7_featureCounts_Control_1.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/MCF7_featureCounts_Control_1.txt Wed May 21 05:03:49 2014 -0400 @@ -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 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4560 5922 7297 7100 7934 7938 +C16orf93 9 43 9 28 7 21 35 22 10 12 9 23 7 16 1792 +ELP1P 4 1 0 3 0 6 4 1 3 2 0 3 1 1 1692 +CXCL11 3 7 6 6 0 6 18 5 6 6 2 1 8 4 1601 +SCARA5 4 9 4 4 2 12 8 5 7 4 7 2 3 10 4151 +C8orf37 87 131 57 156 53 95 164 88 97 72 107 101 111 117 3373 +FAM84B 5481 8342 3000 10024 3519 7661 13278 4406 4519 3334 3943 4526 4974 5268 5481 +LRRC14 303 912 198 756 209 623 716 460 359 469 262 450 287 406 5353 diff -r 87bf067cfc53 -r 7e45df99a6fc test/design_matrix.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/design_matrix.txt Wed May 21 05:03:49 2014 -0400 @@ -0,0 +1,15 @@ +sample-name Treatment +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 diff -r 87bf067cfc53 -r 7e45df99a6fc tool_dependencies.xml --- a/tool_dependencies.xml Wed May 21 04:55:20 2014 -0400 +++ b/tool_dependencies.xml Wed May 21 05:03:49 2014 -0400 @@ -1,7 +1,7 @@ - +