Revision: 10:24a09ca67621

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/deseq2

Miscellaneous

Name: DESeq2

Description: Determines differentially expressed features from count tables

Id: deseq2

Guid: toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39

Version: 2.11.39

Version command string: 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: ")

Display in tool panel: True

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

toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40

toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.39 (this tool)

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)

Requirements:

name	version	type
bioconductor-deseq2	1.14.1	package
r-getopt	1.20.0	package

Functional tests

name	inputs	outputs	required files
Test-1	rep_factorName_0|rep_factorLevel_0|countsFile: ['GSM461179_treat_single.counts', 'GSM461180_treat_paired.counts', 'GSM461181_treat_paired.counts'] normCounts: True 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 pdf: False rep_factorName_0|rep_factorLevel_0|factorLevel: Treated rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated	counts_out: normalized_readcounts.tab deseq_out: deseq2_out.tab	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 normalized_readcounts.tab deseq2_out.tab
Test-2	rep_factorName_0|rep_factorLevel_0|countsFile: ['sailfish_quant_result1.tab', 'sailfish_quant_result2.tab'] pdf: False rep_factorName_0|rep_factorLevel_1|countsFile: ['sailfish_quant_result3.tab', 'sailfish_quant_result4.tab'] tximport|tximport_selector: tximport rep_factorName_0|factorName: Treatment rep_factorName_0|rep_factorLevel_0|factorLevel: Treated rep_factorName_0|rep_factorLevel_1|factorLevel: Untreated tximport|mapping_format|mapping_format_selector: gtf tximport|mapping_format|gtf_file: genes_sub.gtf	deseq_out: deseq2_tximport_out.tab	sailfish_quant_result1.tab sailfish_quant_result2.tab sailfish_quant_result3.tab sailfish_quant_result4.tab genes_sub.gtf deseq2_tximport_out.tab