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

rpt

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

meta:map

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

*index.html:file

Top level report HTML file

index.html

heat_map_corr_plot

meta:map

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

*heat_map_corr_plot.html:file

HTML file combining heatmap and rank correlation plot

heat_map_corr_plot.html

report_tsvs_ref

meta:map

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

*gsea_report_for_${reference}.tsv:file

Main TSV results report file for the reference group.

gsea_report_for_reference*.tsv

report_htmls_ref

meta:map

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

*gsea_report_for_${reference}.html:file

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

gsea_report_for_reference*.html

report_tsvs_target

meta:map

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

*gsea_report_for_${target}.tsv:file

Main TSV results report file for the target group.

gsea_report_for_target*.tsv

report_htmls_target

meta:map

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

*gsea_report_for_${target}.html:file

Main HTML results report file for the target group.

gsea_report_for_target*.html

ranked_gene_list

meta:map

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

*ranked_gene_list*.tsv:file

TSV file with ranked gene list and scores

ranked_gene_list*.tsv

gene_set_sizes

meta:map

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

*gene_set_sizes.tsv:file

TSV file with gene set sizes

gene_set_sizes.tsv

histogram

meta:map

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

*global_es_histogram.png:file

Plot showing number of gene sets by enrichment score

global_es_histogram.png

heatmap

meta:map

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

*heat_map_1.png:file

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

heat_map_1.png

pvalues_vs_nes_plot

meta:map

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

*pvalues_vs_nes_plot.png:file

Plot showing FDR q-value by normalised enrichment score

pvalues_vs_nes_plot

ues_vs_nes_plot:file

Plot showing FDR q-value by normalised enrichment score

pvalues_vs_nes_plot

ranked_list_corr

meta:map

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

*ranked_list_corr_2.png:file

Ranked Gene List Correlation Profile

ranked_list_corr_2.png

butterfly_plot

meta:map

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

*butterfly_plot.png:file

Butterfly plot with gene rank plotted against score

butterfly_plot.png

gene_set_tsv

meta:map

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

*[!gene_set_size|gsea_report|ranked_gene_list]*.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

meta:map

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

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

meta:map

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

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

meta:map

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

*_snapshot*.html:list

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

*_snapshot*.html

gene_set_enplot

meta:map

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

*enplot*.png: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

meta:map

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

*gset_rnd_es_dist*.png: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

meta:map

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

*.zip:file

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

*.zip

versions

versions.yml:file

File containing software versions

versions.yml

Tools

included in
differentialabundance
maintainer
Github user pinin4fjords
get in touch
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