Revision: 12:fa56d93f7980

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/bgruening/diffbind

Miscellaneous

Name: DiffBind

Description: differential binding analysis of ChIP-Seq peak data

Id: diffbind

Guid: toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.2

Version: 2.6.6.2

Version command string: echo $(R --version | grep version | grep -v GNU)", DiffBind version" $(R --vanilla --slave -e "library(DiffBind); cat(sessionInfo()\$otherPkgs\$DiffBind\$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: ")

Display in tool panel: True

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

toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.3

toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.2 (this tool)

toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.1

toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.0

toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.5.0

toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.2.2

toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.2.1

toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.2.0

toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.1.0

toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.0.2

toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.0.1

diffbind

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name	version	type
bioconductor-diffbind	2.6.6	package
r-getopt	1.20.0	package
r-rjson	0.2.15	package

Functional tests

name	inputs	outputs	required files
Test-1	rep_group_1|groupName: Responsive scorecol: 5 out|rdata: True out|rscript: True rep_group_0|bamreads: ['BT474_ER_1.bam', 'BT474_ER_2.bam'] rep_group_1|peaks: ['MCF7_ER_1.bed.gz', 'MCF7_ER_2.bed.gz'] rep_group_0|groupName: Resistant out|binding_matrix: True out|analysis_info: True out|pdf: True rep_group_1|bamreads: ['MCF7_ER_1.bam', 'MCF7_ER_2.bam'] rep_group_0|peaks: ['BT474_ER_1.bed.gz', 'BT474_ER_2.bed.gz']	outfile: out_diffbind.tab plots: out_plots.pdf binding_matrix: out_binding.matrix rdata: DiffBind_analysis.RData rscript: out_rscript.txt analysis_info: out_analysis_info.txt	BT474_ER_1.bed.gz BT474_ER_2.bed.gz BT474_ER_1.bam BT474_ER_2.bam MCF7_ER_1.bed.gz MCF7_ER_2.bed.gz MCF7_ER_1.bam MCF7_ER_2.bam out_diffbind.tab out_plots.pdf out_binding.matrix DiffBind_analysis.RData out_rscript.txt out_analysis_info.txt