differential_functional_enrichment

Run functional analysis on differential abundance analysis output

functional analysisfunctional enrichmentdifferentialover-representation analysis

https://github.com/nf-core/modules/[...]/subworkflows/nf-core/differential_functional_enrichment

Description

Run functional analysis on differential abundance analysis output

Input

name

description

pattern

`ch_input`

Channel with the input data for functional analysis.

input should be the DE statistics obtained from the DE modules, or the
normalised abundance matrix (in the case of running GSEA). genesets is the
gene sets database, in GMT format for all methods. background holds the
background features, currently only required for gprofiler2.
analysis_method is one of gprofiler2, gsea, decoupler or grea.

Structure: [ val(meta), path(input), path(genesets), path(background), val(analysis_method) ]

`ch_contrasts`

Channel with contrast information. meta_contrast holds all the contrast info,
such as contrast id, variable, reference, target, etc.

Structure: [ val(meta), val(meta_contrast), val(variable), val(reference), val(target), val(formula), val(comparison) ]

`ch_samplesheet`

Channel with sample information.

Structure: [ val(meta_exp), path(samplesheet) ]

`ch_featuresheet`

Channel with features information, alongside the features id and features symbol
column names.

Structure: [ val(meta_exp), path(features), val(features_id), val(features_symbol) ]

Output

name

description

pattern

`gprofiler2_plot_html`

HTML file; interactive Manhattan plot of all enriched pathways. Note that this
file will only be generated if enriched pathways were found.

Structure: [ val(meta), path(plot_html) ]

*.gprofiler2.gostplot.html

`gprofiler2_all_enrich`

Table listing all enriched pathways that were found by gprofiler2. It can be
empty, if none is found.

Structure: [ val(meta), path(all_enrich) ]

*.gprofiler2.all_enriched_pathways.tsv

`gprofiler2_sub_enrich`

Table listing enriched pathways that were found from one particular source.
Note that it will only be created if any were found.

Structure: [ val(meta), path(sub_enrich) ]

*.gprofiler2.*.sub_enriched_pathways.tsv

`gprofiler2_artifacts`

PNG file; Manhattan plot of all enriched pathways.

Structure: [ val(meta), path(plot_png) ]

*.gprofiler2.gostplot.png

`gprofiler2_sub_plot`

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

Structure: [ val(meta), path(sub_plot) ]

*.gprofiler2.*.sub_enriched_pathways.png

`gprofiler2_rds`

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

Structure: [ val(meta), path(rds) ]

*.gprofiler2.gost_results.rds

`gprofiler2_filtered_gmt`

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.

Structure: [ val(meta), path(filtered_gmt) ]

*ENSG_filtered.gmt

`gsea_report_tsv`

Main TSV results report files for the reference and target groups.

Structure: [ val(meta), path(report_tsv_ref), path(report_tsv_target) ]

*gsea_report_for_*.tsv

`gsea_report_html`

Main HTML results report files for the reference and target groups.

Structure: [ val(meta), path(report_html_ref), path(report_html_target) ]

*gsea_report_for_*.html

`gsea_index_html`

Top level report HTML file.

Structure: [ val(meta), path(index_html) ]

*index.html

`gsea_heat_map_corr_plot`

HTML file combining heatmap and rank correlation plot.

Structure: [ val(meta), path(heat_map_corr_plot) ]

*heat_map_corr_plot.html

`gsea_ranked_gene_list`

TSV file with ranked gene list and scores.

Structure: [ val(meta), path(ranked_gene_list) ]

*ranked_gene_list*.tsv

`gsea_gene_set_sizes`

TSV file with gene set sizes.

Structure: [ val(meta), path(gene_set_sizes) ]

*gene_set_sizes.tsv

`gsea_histogram`

Plot showing number of gene sets by enrichment score.

Structure: [ val(meta), path(histogram) ]

*global_es_histogram.png

`gsea_heatmap`

Heat map of the top 50 features for each phenotype in the test.

Structure: [ val(meta), path(heatmap) ]

*heat_map_1.png

`gsea_pvalues_vs_nes_plot`

Plot showing FDR q-value by normalised enrichment score.

Structure: [ val(meta), path(pvalues_vs_nes_plot) ]

*pvalues_vs_nes_plot.png

`gsea_ranked_list_corr`

Ranked gene list correlation profile.

Structure: [ val(meta), path(ranked_list_corr) ]

*ranked_list_corr_2.png

`gsea_butterfly_plot`

Butterfly plot with gene rank plotted against score.

Structure: [ val(meta), path(butterfly_plot) ]

*butterfly_plot.png

`gsea_gene_set_tsv`

Where -make_sets is not set to false, TSV files, one file for each gene set,
with detail on enrichment for each gene.

Structure: [ val(meta), [ path(gene_set_tsv) ] ]

gene_sets_*.tsv

`gsea_gene_set_html`

Where -make_sets is not set to false, HTML files, one file for each gene set,
with detail on enrichment for each gene.

Structure: [ val(meta), [ path(gene_set_html) ] ]

gene_sets_*.html

`gsea_gene_set_heatmap`

Where -make_sets is not set to false, PNG-format heatmaps, one file for each
gene set, showing expression for each gene.

Structure: [ val(meta), [ path(gene_set_heatmap) ] ]

gene_sets_*.png

`gsea_gene_set_enplot`

Where -make_sets is not set to false, PNG-format enrichment (barcode) plots, one
file for each gene set, showing how genes contribute to enrichment.

Structure: [ val(meta), [ path(gene_set_enplot) ] ]

*enplot*.png

`gsea_gene_set_dist`

Where -make_sets is not set to false, PNG-format enrichment score distribution
plots, one file for each gene set.

Structure: [ val(meta), [ path(gene_set_dist) ] ]

*gset_rnd_es_dist*.png

`gsea_snapshot`

HTML files, one each for positive and negative enrichment, collecting elements
of gsea_gene_set_enplot.

Structure: [ val(meta), [ path(snapshot) ] ]

*_snapshot*.html

`gsea_archive`

Where -zip_report is set, a zip archive containing all GSEA outputs.

Structure: [ val(meta), path(archive) ]

*.zip

`gsea_rpt`

File containing the parameter settings used by GSEA.

Structure: [ val(meta), path(rpt) ]

*.rpt

`decoupler_dc_estimate`

Files containing the estimation results of the enrichment(s).

Structure: [ val(meta), path(estimate_files) ]

*estimate_decoupler.tsv

`decoupler_dc_pvals`

Files containing the p-values associated to the estimation results of the
enrichment(s).

Structure: [ val(meta), path(pvals_files) ]

*pvals_decoupler.tsv

`decoupler_png`

Files containing the plots associated to the estimation results of the
enrichment(s).

Structure: [ val(meta), path(plot_files) ]

*estimate_decoupler_plot.png

`grea_results`

Main TSV results file from GREA.

Structure: [ val(meta), path(results) ]

*.grea.tsv

`session_info`

Log file containing information about the R session that was run for gprofiler2.

Structure: [ val(meta), path(session_info) ]

*R_sessionInfo.log

differential_functional_enrichment

Description

Input

ch_input

ch_contrasts

ch_samplesheet

ch_featuresheet

Output

gprofiler2_plot_html

gprofiler2_all_enrich

gprofiler2_sub_enrich

gprofiler2_artifacts

gprofiler2_sub_plot

gprofiler2_rds

gprofiler2_filtered_gmt

gsea_report_tsv

gsea_report_html

gsea_index_html

gsea_heat_map_corr_plot

gsea_ranked_gene_list

gsea_gene_set_sizes

gsea_histogram

gsea_heatmap

gsea_pvalues_vs_nes_plot

gsea_ranked_list_corr

gsea_butterfly_plot

gsea_gene_set_tsv

gsea_gene_set_html

gsea_gene_set_heatmap

gsea_gene_set_enplot

gsea_gene_set_dist

gsea_snapshot

gsea_archive

gsea_rpt

decoupler_dc_estimate

decoupler_dc_pvals

decoupler_png

grea_results

session_info

included in

included modules and subworkflows

maintainers

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