Repository revision
21:a6fc9228e1a0

Repository 'deseq2'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/deseq2

DESeq2 tool metadata
Miscellaneous
DESeq2
Determines differentially expressed features from count tables
deseq2
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.5
2.11.40.5
echo $(R --version | grep version | grep -v GNU)", DESeq2 version" $(R --vanilla --slave -e "library(DESeq2); cat(sessionInfo()\$otherPkgs\$DESeq2\$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/deseq2/deseq2/2.11.40.6
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.5 (this tool)
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.4
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.3
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.2
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.1
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.38
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.4
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.3
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.2
toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.1.8.0
deseq2
Requirements (dependencies defined in the <requirements> tag set)
name version type
bioconductor-deseq2 1.20.0 package
bioconductor-rhdf5 2.24.0 package
bioconductor-tximport 1.8.0 package
bioconductor-genomicfeatures 1.32.3 package
r-getopt 1.20.2 package
r-ggrepel 0.8.0 package
r-gplots 3.0.1 package
r-pheatmap 1.0.10 package
r-rjson 0.2.20 package
Functional tests
name inputs outputs required files
Test-1 normVST: True
rep_factorName_0|rep_factorLevel_0|countsFile: ['GSM461179_treat_single.counts', 'GSM461180_treat_paired.counts', 'GSM461181_treat_paired.counts']
rep_factorName_0|rep_factorLevel_1|countsFile: ['GSM461176_untreat_single.counts', 'GSM461177_untreat_paired.counts', 'GSM461178_untreat_paired.counts', 'GSM461182_untreat_single.counts']
rep_factorName_0|factorName: Treatment
normCounts: True
pdf: False
rep_factorName_0|rep_factorLevel_0|factorLevel: Treated
rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated
normRLog: True
 attributes: name
attributes: name
attributes: name
attributes: name
 GSM461179_treat_single.counts
GSM461180_treat_paired.counts
GSM461181_treat_paired.counts
GSM461176_untreat_single.counts
GSM461177_untreat_paired.counts
GSM461178_untreat_paired.counts
GSM461182_untreat_single.counts
name
Test-2 rep_factorName_0|rep_factorLevel_0|countsFile: ['GSM461179_treat_single.counts', 'GSM461180_treat_paired.counts', 'GSM461181_treat_paired.counts']
rep_factorName_0|rep_factorLevel_1|countsFile: ['GSM461176_untreat_single.counts', 'GSM461177_untreat_paired.counts', 'GSM461178_untreat_paired.counts', 'GSM461182_untreat_single.counts']
rep_factorName_0|factorName: Treatment
normCounts: True
batch_factors: batch_factors.tab
pdf: False
rep_factorName_0|rep_factorLevel_0|factorLevel: Treated
rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated
 attributes: name
 GSM461179_treat_single.counts
GSM461180_treat_paired.counts
GSM461181_treat_paired.counts
GSM461176_untreat_single.counts
GSM461177_untreat_paired.counts
GSM461178_untreat_paired.counts
GSM461182_untreat_single.counts
batch_factors.tab
name
Test-3 normVST: True
rep_factorName_0|rep_factorLevel_0|countsFile: ['GSM461179_treat_single.counts.noheader', 'GSM461180_treat_paired.counts.noheader', 'GSM461181_treat_paired.counts.noheader']
rep_factorName_0|rep_factorLevel_1|countsFile: ['GSM461176_untreat_single.counts.noheader', 'GSM461177_untreat_paired.counts.noheader', 'GSM461178_untreat_paired.counts.noheader', 'GSM461182_untreat_single.counts.noheader']
header: False
normCounts: True
pdf: False
rep_factorName_0|factorName: Treatment
rep_factorName_0|rep_factorLevel_0|factorLevel: Treated
rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated
normRLog: True
 attributes: name
attributes: name
attributes: name
attributes: name
 GSM461179_treat_single.counts.noheader
GSM461180_treat_paired.counts.noheader
GSM461181_treat_paired.counts.noheader
GSM461176_untreat_single.counts.noheader
GSM461177_untreat_paired.counts.noheader
GSM461178_untreat_paired.counts.noheader
GSM461182_untreat_single.counts.noheader
name
Test-4 rep_factorName_0|rep_factorLevel_0|countsFile: ['sailfish/sailfish_quant.sf1.tab', 'sailfish/sailfish_quant.sf2.tab', 'sailfish/sailfish_quant.sf3.tab']
rep_factorName_0|rep_factorLevel_1|countsFile: ['sailfish/sailfish_quant.sf4.tab', 'sailfish/sailfish_quant.sf5.tab', 'sailfish/sailfish_quant.sf6.tab']
tximport|tximport_selector: tximport
tximport|mapping_format|tabular_file: tx2gene.tab
rep_factorName_0|factorName: Treatment
tximport|txtype: sailfish
pdf: False
rep_factorName_0|rep_factorLevel_0|factorLevel: Treated
rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated
tximport|mapping_format|mapping_format_selector: tabular
 attributes: name
 sailfish/sailfish_quant.sf1.tab
sailfish/sailfish_quant.sf2.tab
sailfish/sailfish_quant.sf3.tab
sailfish/sailfish_quant.sf4.tab
sailfish/sailfish_quant.sf5.tab
sailfish/sailfish_quant.sf6.tab
tx2gene.tab
name
Test-5 rep_factorName_0|rep_factorLevel_0|countsFile: ['sailfish/sailfish_quant.sf1.tab', 'sailfish/sailfish_quant.sf2.tab', 'sailfish/sailfish_quant.sf3.tab']
rep_factorName_0|rep_factorLevel_1|countsFile: ['sailfish/sailfish_quant.sf4.tab', 'sailfish/sailfish_quant.sf5.tab', 'sailfish/sailfish_quant.sf6.tab']
tximport|tximport_selector: tximport
tximport|mapping_format|gtf_file: GRCh38_latest_genomic.gff
rep_factorName_0|factorName: Treatment
tximport|txtype: sailfish
pdf: False
rep_factorName_0|rep_factorLevel_0|factorLevel: Treated
rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated
tximport|mapping_format|mapping_format_selector: gtf
 attributes: name
 sailfish/sailfish_quant.sf1.tab
sailfish/sailfish_quant.sf2.tab
sailfish/sailfish_quant.sf3.tab
sailfish/sailfish_quant.sf4.tab
sailfish/sailfish_quant.sf5.tab
sailfish/sailfish_quant.sf6.tab
GRCh38_latest_genomic.gff
name
Test-6 rep_factorName_0|rep_factorLevel_0|countsFile: ['sailfish_ensembl/sailfish_quant.sf1.tab', 'sailfish_ensembl/sailfish_quant.sf2.tab', 'sailfish_ensembl/sailfish_quant.sf3.tab']
rep_factorName_0|rep_factorLevel_1|countsFile: ['sailfish_ensembl/sailfish_quant.sf4.tab', 'sailfish_ensembl/sailfish_quant.sf5.tab', 'sailfish_ensembl/sailfish_quant.sf6.tab']
tximport|tximport_selector: tximport
tximport|mapping_format|gtf_file: Homo_sapiens.GRCh38.94.gtf
rep_factorName_0|factorName: Treatment
tximport|txtype: sailfish
pdf: False
rep_factorName_0|rep_factorLevel_0|factorLevel: Treated
rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated
tximport|mapping_format|mapping_format_selector: gtf
 attributes: name
 sailfish_ensembl/sailfish_quant.sf1.tab
sailfish_ensembl/sailfish_quant.sf2.tab
sailfish_ensembl/sailfish_quant.sf3.tab
sailfish_ensembl/sailfish_quant.sf4.tab
sailfish_ensembl/sailfish_quant.sf5.tab
sailfish_ensembl/sailfish_quant.sf6.tab
Homo_sapiens.GRCh38.94.gtf
name