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Revision: 15:5bf899c13979

Repository 'edger'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/edger

edgeR tool metadata

Miscellaneous

Name: edgeR

Description: Perform differential expression of count data

Id: edger

Guid: toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy4

Version: 3.36.0+galaxy4

Version command string: 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: ")

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy4 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy3

toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy2

toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy1

toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.34.0+galaxy2

toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.34.0+galaxy1

toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.34.0

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

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)

Requirements:

name

version

type

bioconductor-edger

3.36.0

package

bioconductor-limma

3.50.0

package

r-rjson

0.2.20

package

r-getopt

1.20.3

package

r-statmod

1.4.36

package

r-scales

1.1.1

package

Functional tests

name

inputs

outputs

required files

Test-1

input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|rep_contrast_1|contrast: WT-Mut
contrasts|contrastOpt: manual
adv|normalisationOption: TMM

name: value

matrix.txt
value

Test-2

input|counts: matrix-complex.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: MutA,MutA,MutA,MutB,MutB,MutB,WTA,WTA,WTA,WTB,WTB,WTB
input|format: matrix
contrasts|rep_contrast_0|contrast: (MutA-MutB)-(WTA-WTB)
contrasts|contrastOpt: manual
adv|normalisationOption: TMM

name: value

matrix-complex.txt
value

Test-3

input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
anno|geneanno: anno.txt
anno|annoOpt: yes
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
adv|normalisationOption: TMM

matrix.txt
anno.txt

Test-4

input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
out|rscript: True
out|rdaOption: True
adv|normalisationOption: TMM

name: value
name: value

matrix.txt
value

Test-5

input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|fact|rep_factor_1|factorName: Batch
input|fact|rep_factor_1|groupNames: b1,b2,b3,b1,b2,b3
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
adv|normalisationOption: TMM

matrix.txt

Test-6

input|counts: matrix.txt
input|fact|finfo: factorinfo.txt
input|fact|ffile: yes
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
adv|normalisationOption: TMM

matrix.txt
factorinfo.txt

Test-7

input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
out|normCounts: True
adv|normalisationOption: TMM

matrix.txt

Test-8

input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
adv|normalisationOption: TMM
adv|lrtOption: True

name: value

matrix.txt
value

Test-9

input|rep_factor_0|factorName: Genotype
input|rep_factor_0|rep_group_0|groupName: WT
input|rep_factor_0|rep_group_0|countsFile: ['WT1.counts', 'WT2.counts', 'WT3.counts']
input|rep_factor_0|rep_group_1|groupName: Mut
input|rep_factor_0|rep_group_1|countsFile: ['Mut1.counts', 'Mut2.counts', 'Mut3.counts']
input|rep_factor_1|factorName: Batch
input|rep_factor_1|rep_group_0|groupName: b1
input|rep_factor_1|rep_group_0|countsFile: ['WT1.counts', 'Mut1.counts']
input|rep_factor_1|rep_group_1|groupName: b2
input|rep_factor_1|rep_group_1|countsFile: ['WT2.counts', 'Mut2.counts']
input|rep_factor_1|rep_group_2|groupName: b3
input|rep_factor_1|rep_group_2|countsFile: ['WT3.counts', 'Mut3.counts']
input|format: files
anno|geneanno: anno.txt
anno|annoOpt: yes
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|rep_contrast_1|contrast: WT-Mut
contrasts|contrastOpt: manual
out|normCounts: True

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-10

input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
f|filt|cformat|cpmReq: 1000
f|filt|cformat|cpmSampleReq: 3
f|filt|cformat|format_select: cpm
f|filt|filt_select: yes
adv|normalisationOption: TMM

name: value

matrix.txt
value

Test-11

input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
f|filt|cformat|cntReq: 10
f|filt|cformat|samples|cntSampleReq: 3
f|filt|cformat|samples|count_select: sample
f|filt|cformat|format_select: counts
f|filt|filt_select: yes
adv|normalisationOption: TMM

name: value

matrix.txt
value

Test-12

input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|format: matrix
contrasts|rep_contrast_0|contrast: Mut-WT
contrasts|contrastOpt: manual
f|filt|cformat|cntReq: 1000
f|filt|cformat|samples|count_select: total
f|filt|cformat|format_select: counts
f|filt|filt_select: yes
adv|normalisationOption: TMM

name: value

matrix.txt
value

Test-13

input|counts: matrix.txt
input|fact|rep_factor_0|factorName: Genotype
input|fact|rep_factor_0|groupNames: Mut,Mut,Mut,WT,WT,WT
input|fact|rep_factor_1|factorName: Batch
input|fact|rep_factor_1|groupNames: b1,b2,b3,b1,b2,b3
input|format: matrix
formula: ~ 0 + Genotype + Batch
contrasts|cinfo: contrasts_file.txt
contrasts|contrastOpt: file
adv|normalisationOption: TMM

matrix.txt
contrasts_file.txt