Repository revision
25:d6f5fa4ee473

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

limma tool metadata
Miscellaneous
limma
Perform differential expression with limma-voom or limma-trend
limma_voom
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0
3.50.1+galaxy0
echo $(R --version | grep version | grep -v GNU)", limma version" $(R --vanilla --slave -e "library(limma); cat(sessionInfo()\$otherPkgs\$limma\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", edgeR version" $(R --vanilla --slave -e "library(edgeR); cat(sessionInfo()\$otherPkgs\$edgeR\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", statmod version" $(R --vanilla --slave -e "library(statmod); cat(sessionInfo()\$otherPkgs\$statmod\$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: ")", gplots version" $(R --vanilla --slave -e "library(gplots); cat(sessionInfo()\$otherPkgs\$gplots\$Version)" 2> /dev/null | grep -v -i "WARNING: ")", Glimma version" $(R --vanilla --slave -e "library(Glimma); cat(sessionInfo()\$otherPkgs\$Glimma\$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/limma_voom/limma_voom/3.58.1+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.1+galaxy0 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.50.0+galaxy0
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.48.0+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.48.0+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.48.0
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy3
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy2
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3+galaxy1
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.38.3
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.36.5
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.10
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.9
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.8
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.7
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.6
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.5
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.4
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.3
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.2
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.1
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.9.0
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/3.34.6.0
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/1.2.0
toolshed.g2.bx.psu.edu/repos/iuc/limma_voom/limma_voom/1.1.1
limma_voom
Requirements (dependencies defined in the <requirements> tag set)
name version type
bioconductor-limma 3.50.1 package
bioconductor-edger 3.36.0 package
r-statmod 1.4.36 package
r-scales 1.1.1 package
r-rjson 0.2.21 package
r-getopt 1.20.3 package
r-gplots 3.1.1 package
bioconductor-glimma 2.4.0 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
cont|rep_contrast_0|contrast: Mut-WT
cont|rep_contrast_1|contrast: WT-Mut
cont|cfile: no
adv|topgenes: 6
adv|normalisationOption: TMM
name: value
matrix.txt
value
Test-2 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
cont|rep_contrast_0|contrast: Mut-WT
cont|cfile: no
adv|topgenes: 6
adv|normalisationOption: TMM
matrix.txt
anno.txt
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
cont|rep_contrast_0|contrast: Mut-WT
cont|cfile: no
out|rscript: True
out|rdaOption: True
adv|topgenes: 6
adv|normalisationOption: TMM
name: value
name: value
matrix.txt
value
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|fact|rep_factor_1|factorName: Batch
input|fact|rep_factor_1|groupNames: b1,b2,b3,b1,b2,b3
input|format: matrix
cont|rep_contrast_0|contrast: Mut-WT
cont|cfile: no
adv|topgenes: 6
adv|normalisationOption: TMM
matrix.txt
Test-5 input|counts: matrix.txt
input|fact|finfo: factorinfo.txt
input|fact|ffile: yes
input|format: matrix
cont|rep_contrast_0|contrast: Mut-WT
cont|cfile: no
adv|topgenes: 6
adv|normalisationOption: TMM
matrix.txt
factorinfo.txt
Test-6 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
cont|rep_contrast_0|contrast: Mut-WT
cont|cfile: no
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
out|filtCounts: True
out|normCounts: True
adv|topgenes: 6
adv|normalisationOption: TMM
name: value
name: value
matrix.txt
value
Test-7 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
cont|rep_contrast_0|contrast: Mut-WT
cont|rep_contrast_1|contrast: WT-Mut
cont|cfile: no
out|normCounts: True
adv|topgenes: 6
name: value
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
value
Test-8 deMethod|de_select: trend
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
cont|rep_contrast_0|contrast: Mut-WT
cont|cfile: no
adv|topgenes: 6
adv|normalisationOption: TMM
name: value
matrix.txt
value
Test-9 deMethod|de_select: trend
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
cont|rep_contrast_0|contrast: Mut-WT
cont|cfile: no
adv|topgenes: 6
adv|normalisationOption: TMM
name: value
matrix.txt
anno.txt
value
Test-10 deMethod|de_select: voom
input|counts: matrix_num.txt
input|fact|rep_factor_0|factorName: Group
input|fact|rep_factor_0|groupNames: 2,2,2,1,1,1
input|format: matrix
anno|geneanno: anno.txt
anno|annoOpt: yes
cont|rep_contrast_0|contrast: 2-1
cont|cfile: no
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
out|normCounts: True
adv|topgenes: 6
adv|normalisationOption: TMM
name: value
matrix_num.txt
anno.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
cont|cinfo: contrasts.txt
cont|cfile: yes
adv|topgenes: 6
adv|normalisationOption: TMM
matrix.txt
contrasts.txt