modules/gprofiler2_gost

runs a functional enrichment analysis with gprofiler2

gene set analysisenrichmentgprofiler2gostgene set

https://github.com/nf-core/modules/[...]/modules/nf-core/gprofiler2/gost

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}

`gmt_file:file`

Path to a GMT file downloaded from g

that should be queried instead of the online databases

*.gmt

`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

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

modules/gprofiler2_gost

Description

Input

`meta:map`

`de_file:file`

`gmt_file:file`

`background_file:file`

Output

`all_enrich`

`meta:map`

`*.gprofiler2.all_enriched_pathways.tsv:file`

`rds`

`meta:map`

`*.gprofiler2.gost_results.rds:file`

`plot_png`

`meta:map`

`*.gprofiler2.gostplot.png:file`

`plot_html`

`meta:map`

`*.gprofiler2.gostplot.html:file`

`sub_enrich`

`meta:map`

`.gprofiler2..sub_enriched_pathways.tsv:file`

`sub_plot`

`meta:map`

`.gprofiler2..sub_enriched_pathways.png:file`

`filtered_gmt`

`meta:map`

`*ENSG_filtered.gmt:file`

`session_info`

`meta:map`

`*R_sessionInfo.log:file`

`versions`

`versions.yml:file`

Tools

gprofiler2
GPL v2

included in

maintainer

get in touch

modules/gprofiler2_gost

Description

Input

meta:map

de_file:file

gmt_file:file

background_file:file

Output

all_enrich

meta:map

*.gprofiler2.all_enriched_pathways.tsv:file

rds

meta:map

*.gprofiler2.gost_results.rds:file

plot_png

meta:map

*.gprofiler2.gostplot.png:file

plot_html

meta:map

*.gprofiler2.gostplot.html:file

sub_enrich

meta:map

*.gprofiler2.*.sub_enriched_pathways.tsv:file

sub_plot

meta:map

*.gprofiler2.*.sub_enriched_pathways.png:file

filtered_gmt

meta:map

*ENSG_filtered.gmt:file

session_info

meta:map

*R_sessionInfo.log:file

versions

versions.yml:file

Tools

gprofiler2 GPL v2

included in

maintainer

get in touch

`meta:map`

`de_file:file`

`gmt_file:file`

`background_file:file`

`all_enrich`

`meta:map`

`*.gprofiler2.all_enriched_pathways.tsv:file`

`rds`

`meta:map`

`*.gprofiler2.gost_results.rds:file`

`plot_png`

`meta:map`

`*.gprofiler2.gostplot.png:file`

`plot_html`

`meta:map`

`*.gprofiler2.gostplot.html:file`

`sub_enrich`

`meta:map`

`.gprofiler2..sub_enriched_pathways.tsv:file`

`sub_plot`

`meta:map`

`.gprofiler2..sub_enriched_pathways.png:file`

`filtered_gmt`

`meta:map`

`*ENSG_filtered.gmt:file`

`session_info`

`meta:map`

`*R_sessionInfo.log:file`

`versions`

`versions.yml:file`

gprofiler2
GPL v2