Skip to content
Permalink
Browse files
Added genesets as raw data files
  • Loading branch information
jenzopr committed Jul 17, 2015
1 parent aa20511 commit 916de7e3f30bd24574d8d31c345931183dc2f643
@@ -45,6 +45,16 @@
#for $custom in $customs
-r $custom.cr
#end for
#set $g=str($genesets).split(",")
#for $geneset in $g
#set global $gs=$geneset
-g ${ filter( lambda x: str( x[0] ) == str( $gs ), $__app__.tool_data_tables[ 'admire_genesets' ].get_fields() )[0][-1] }
#end for
#end if
#for $cugs in $cu_genesets
-g $cugs.cu
#end for
-i $n_images
-o $o_compressed > $o_log
</command>
<inputs>
@@ -102,6 +112,7 @@
<param name="det_p" label="Detection p-value threshold for failed probe identification" type="float" min="0" max="1" value="0.01" help="Mark a probes as failed, if it has a detection p-value higher than the given value. Failed probes can be excluded from subsequent analysis using the failed sample threshold (see below)." />
<param name="s_thresh" label="Failed sample threshold" type="float" min="0" max="1" value="0.4" help="Probes are excluded from subsequent analysis if the proportion of failed probes across all samples is higher than the given value." />
<param name="fdr" label="Q-value cutoff for multiple testing" type="float" min="0" max="1" value="0.05" help="Definde a false discovery rate to limit results after multiple testing correction." />
<param name="n_images" label="Number of additional plots for n best regions" type="integer" value="20" max="50" min="0" help="Prints n bubble plots for the best (i.e. most significant) regions into the visualization directory." />
<param name="regions" type="select" label="Select genomic regions to test" display="checkboxes" multiple="true" help="Regions will be overlapped with GC probes and significant different methylated regions will be reported.">
<options from_data_table="admire_regions" />
</param>
@@ -0,0 +1,14 @@
c1.all c1.all C1: Positional gene sets (by chromosome, 326) genesets/c1.all.v5.0.symbols.gmt
c2.cgp c2.cgp C2: Chemical and genetic pertubations (3395) genesets/c2.cpg.v5.0.symbols.gmt
c2.cp.biocarta c2.cp.biocarta C2: BioCharta canonical pathways (217) genesets/c2.cp.biocarta.v5.0.symbols.gmt
c2.cp.kegg c2.cp.kegg C2: KEGG gene sets (186) genesets/c2.cp.kegg.v5.0.symbols.gmt
c2.cp.reactome c2.cp.reactome C2: Reactome gene sets (674) genesets/c2.cp.reactome.v5.0.symbols.gmt
c3.tft c3.tft C3: transcription factor targets (615) genesets/c3.tft.v5.0.symbols.gmt
c4.cgn c4.cgn C4: Cancer gene neighborhoods (427) genesets/c4.cgn.v5.0.symbols.gmt
c4.cm c4.cm C4: Cancer modules (431) genesets/c4.cm.v5.0.symbols.gmt
c5.bp c5.bp C5: GO biological process (825) genesets/c5.bp.v5.0.symbols.gmt
c5.cc c5.cc C5: GO cellular component (233) genesets/c5.cc.v5.0.symbols.gmt
c5.mf c5.mf C5: GO molecular function (396) genesets/c5.mf.v5.0.symbols.gmt
c6 c6 C6: Oncogenic signatures (189) genesets/c6.all.v5.0.symbols.gmt
c7 c7 C7: Immunologic signatures (1910) genesets/c7.all.v5.0.symbols.gmt
h h H: Hallmark gene sets (50) genesets/h.all.v5.0.symbols.gmt

Large diffs are not rendered by default.

Large diffs are not rendered by default.

Large diffs are not rendered by default.

Large diffs are not rendered by default.

Large diffs are not rendered by default.

Large diffs are not rendered by default.

Large diffs are not rendered by default.

Large diffs are not rendered by default.

Large diffs are not rendered by default.

Large diffs are not rendered by default.

Large diffs are not rendered by default.

Large diffs are not rendered by default.

Large diffs are not rendered by default.

Large diffs are not rendered by default.

Large diffs are not rendered by default.

0 comments on commit 916de7e

Please sign in to comment.