Repository revision
6:555659de7321

Repository 'edger'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/edger

edgeR tool metadata
Miscellaneous
edgeR
Perform differential expression of count data
edger
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1
3.24.1
echo $(R --version | grep version | grep -v GNU)", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", scales version" $(R --vanilla --slave -e "library(scales); cat(sessionInfo()\$otherPkgs\$scales\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", rjson version" $(R --vanilla --slave -e "library(rjson); cat(sessionInfo()\$otherPkgs\$rjson\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", getopt version" $(R --vanilla --slave -e "library(getopt); cat(sessionInfo()\$otherPkgs\$getopt\$Version)" 2> /dev/null | grep -v -i "WARNING: ")
True
Version lineage of this tool (guids ordered most recent to oldest)
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.24.1 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.22.5
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.20.7.2
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.20.7.1
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.20.7.0
toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.16.5
edger
Requirements (dependencies defined in the <requirements> tag set)
name version type
bioconductor-edger 3.24.1 package
bioconductor-limma 3.38.3 package
r-rjson 0.2.20 package
r-getopt 1.20.2 package
r-statmod 1.4.30 package
r-scales 1.0.0 package
Functional tests
name inputs outputs required files
Test-1 rep_contrast_1|contrast: WT-Mut
input|format: matrix
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
adv|normalisationOption: TMM
rep_contrast_0|contrast: Mut-WT
 attributes: name
 matrix.txt
name
Test-2 anno|geneanno: anno.txt
anno|annoOpt: yes
input|format: matrix
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
adv|normalisationOption: TMM
rep_contrast_0|contrast: Mut-WT
 matrix.txt
anno.txt
Test-3 adv|normalisationOption: TMM
out|rscript: True
input|format: matrix
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|counts: matrix.txt
out|rdaOption: True
input|fact|rep_factor_0|factorName: Genotype
rep_contrast_0|contrast: Mut-WT
 attributes: name
attributes: name
 matrix.txt
name
Test-4 input|fact|rep_factor_0|factorName: Genotype
adv|normalisationOption: TMM
input|format: matrix
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|counts: matrix.txt
input|fact|rep_factor_1|factorName: Batch
input|fact|rep_factor_1|groupNames: b1,b2,b3,b1,b2,b3
rep_contrast_0|contrast: Mut-WT
 matrix.txt
Test-5 adv|normalisationOption: TMM
input|format: matrix
input|counts: matrix.txt
input|fact|ffile: yes
input|fact|finfo: factorinfo.txt
rep_contrast_0|contrast: Mut-WT
 matrix.txt
factorinfo.txt
Test-6 adv|normalisationOption: TMM
input|format: matrix
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
rep_contrast_0|contrast: Mut-WT
out|normCounts: True
 matrix.txt
Test-7 adv|normalisationOption: TMM
input|format: matrix
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
adv|lrtOption: True
rep_contrast_0|contrast: Mut-WT
 attributes: name
 matrix.txt
name
Test-8 input|rep_factor_0|rep_group_0|groupName: WT
input|rep_factor_1|factorName: Batch
anno|annoOpt: yes
input|rep_factor_1|rep_group_0|groupName: b1
input|rep_factor_1|rep_group_2|groupName: b3
input|rep_factor_0|rep_group_1|groupName: Mut
input|rep_factor_0|rep_group_1|countsFile: ['Mut1.counts', 'Mut2.counts', 'Mut3.counts']
anno|geneanno: anno.txt
input|rep_factor_0|rep_group_0|countsFile: ['WT1.counts', 'WT2.counts', 'WT3.counts']
input|rep_factor_1|rep_group_0|countsFile: ['WT1.counts', 'Mut1.counts']
rep_contrast_1|contrast: WT-Mut
rep_contrast_0|contrast: Mut-WT
out|normCounts: True
input|rep_factor_0|factorName: Genotype
input|rep_factor_1|rep_group_2|countsFile: ['WT3.counts', 'Mut3.counts']
input|rep_factor_1|rep_group_1|countsFile: ['WT2.counts', 'Mut2.counts']
input|rep_factor_1|rep_group_1|groupName: b2
input|format: files
 WT1.counts
WT2.counts
WT3.counts
Mut1.counts
Mut2.counts
Mut3.counts
WT1.counts
Mut1.counts
WT2.counts
Mut2.counts
WT3.counts
Mut3.counts
anno.txt
Test-9 adv|normalisationOption: TMM
input|format: matrix
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|counts: matrix.txt
f|filt|filt_select: yes
f|filt|cformat|cpmReq: 1000
f|filt|cformat|format_select: cpm
input|fact|rep_factor_0|factorName: Genotype
rep_contrast_0|contrast: Mut-WT
f|filt|cformat|cpmSampleReq: 3
 attributes: name
 matrix.txt
name
Test-10 f|filt|cformat|cntReq: 10
input|format: matrix
f|filt|cformat|format_select: counts
input|counts: matrix.txt
f|filt|filt_select: yes
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
f|filt|cformat|samples|cntSampleReq: 3
input|fact|rep_factor_0|factorName: Genotype
f|filt|cformat|samples|count_select: sample
adv|normalisationOption: TMM
rep_contrast_0|contrast: Mut-WT
 attributes: name
 matrix.txt
name
Test-11 f|filt|cformat|cntReq: 1000
f|filt|cformat|samples|totReq: True
input|format: matrix
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|counts: matrix.txt
f|filt|filt_select: yes
f|filt|cformat|format_select: counts
input|fact|rep_factor_0|factorName: Genotype
f|filt|cformat|samples|count_select: total
adv|normalisationOption: TMM
rep_contrast_0|contrast: Mut-WT
 attributes: name
 matrix.txt
name