Description

run the Broad Gene Set Enrichment tool in GSEA mode

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing metadata, at a minimum an id e.g. [ id:‘test’ ].

gct (file)

GCT file with expression values

*.{gct}

cls (file)

CL file with the classes of the samples in the GCT file

*.{gct}

gene_sets (file)

GMX or GMT file with gene sets

*.{gmx,gmt}

reference (string)

String indicating which of the classes in the cls file should be used
as the reference level of the comparison.

target (string)

String indicating which of the classes in the cls file should be used
as the target level of the comparison.

chip (file)

optional Broad-style chip file mapping identifiers in gct to
those in gene_sets

*.{chip}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing metadata, at a minimum an id e.g. [ id:‘test’ ]

rpt (file)

File containing parameter settings used

*.rpt

index_html (file)

Top level report HTML file

index.html

heat_map_corr_plot (file)

HTML file combining heatmap and rank correlation plot

heat_map_corr_plot.html

report_tsvs_ref (file)

Main TSV results report file for the reference group.

gsea_report_for_reference*.tsv

report_htmls_ref (file)

Main HTML results report file for the reference group. sample groups

gsea_report_for_reference*.html

report_tsvs_target (file)

Main TSV results report file for the target group.

gsea_report_for_target*.tsv

report_htmls_target (file)

Main HTML results report file for the target group.

gsea_report_for_target*.html

ranked_gene_list (file)

TSV file with ranked gene list and scores

ranked_gene_list*.tsv

gene_set_sizes (file)

TSV file with gene set sizes

gene_set_sizes.tsv

butterfly_plot (file)

Butterfly plot with gene rank plotted against score

butterfly_plot.png

histogram (file)

Plot showing number of gene sets by enrichment score

global_es_histogram.png

heatmap (file)

Heat Map of the top 50 features for each phenotype in test

heat_map_1.png

pvalues_vs_nes_plot (file)

Plot showing FDR q-value by normalised enrichment score

pvalues_vs_nes_plot

ranked_list_corr (file)

Ranked Gene List Correlation Profile

ranked_list_corr_2.png

gene_set_tsv (list)

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

[!gene_set_size|gsea_report|ranked_gene_list]*.tsv

gene_set_html (list)

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

[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html

gene_set_heatmap (list)

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

[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png

snapshot (list)

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

*_snapshot*.html

gene_set_enplot (list)

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.

enplot*.png

gene_set_dist (list)

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

gset_rnd_es_dist*.png

archive (file)

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

*.zip

versions (file)

File containing software versions

versions.yml
included in
differentialabundance
maintainer
Github user pinin4fjords
get in touch
Ask a question on Slack Open an issue on GitHub

Tools