Description

runs a functional enrichment analysis with gprofiler2

Input

name:type
description
pattern

meta:map

Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]

de_file:file

CSV or TSV-format tabular file with differential analysis outputs

*.{csv,tsv}

meta2:map

Groovy map

gmt_file:file

Path to a GMT file downloaded from g:profiler that should be queried instead of the online databases

*.gmt

meta3:map

Groovy map

background_file:file

Path to a CSV/TSV/TXT file listing gene IDs that should be used as the background (will override count_file). This can be an expression matrix (see also background_column parameter); if so, will only consider those genes with an expression value > 0 in at least one sample. Alternatively, this can be a TXT file containing only a list of gene IDs.

*.{csv,tsv,txt}

Output

name:type
description
pattern

all_enrich

meta:map

Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]

*.gprofiler2.all_enriched_pathways.tsv:file

TSV file; table listing all enriched pathways that were found. This table will always be created (empty if no enrichment was found), the other output files are only created if enriched pathways were found

*gprofiler2.*all_enriched_pathways.tsv

rds

meta:map

Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]

*.gprofiler2.gost_results.rds:file

RDS file; R object containing the results of the gost query

*gprofiler2.*gost_results.rds

plot_png

meta:map

Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]

*.gprofiler2.gostplot.png:file

PNG file; Manhattan plot of all enriched pathways

*gprofiler2.*gostplot.png

plot_html

meta:map

Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]

*.gprofiler2.gostplot.html:file

HTML file; interactive Manhattan plot of all enriched pathways

*gprofiler2.*gostplot.html

sub_enrich

meta:map

Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]

*.gprofiler2.*.sub_enriched_pathways.tsv:file

TSV file; table listing enriched pathways that were found from one particular source

*gprofiler2.*sub_enriched_pathways.tsv

sub_plot

meta:map

Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]

*.gprofiler2.*.sub_enriched_pathways.png:file

PNG file; bar plot showing the fraction of genes that were found enriched in each pathway

*gprofiler2.*sub_enriched_pathways.png

filtered_gmt

meta:map

Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]

*ENSG_filtered.gmt:file

GMT file that was provided as input or that was downloaded from g:profiler if no input GMT file was given; filtered for the selected datasources

*ENSG_filtered.gmt

session_info

meta:map

Groovy Map containing contrast information, e.g. [ variable:‘treatment’, reference:‘treated’, control:‘saline’, blocking:” ]

*R_sessionInfo.log:file

Log file containing information about the R session that was run for this module

*R_sessionInfo.log

versions

versions.yml:file

File containing software versions

versions.yml

Tools

gprofiler2
GPL v2

An R interface corresponding to the 2019 update of g:Profiler web tool.

biit.cs.ut.ee/gprofiler/page/r rdrr.io/cran/gprofiler2 https://gl.cs.ut.ee/biit/r-gprofiler2 10.1093/nar/gkad347
differentialabundance
Github user WackerO
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