run the Broad Gene Set Enrichment tool in GSEA mode
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
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.
meta2:map
Groovy map
chip:file
optional Broad-style chip file mapping identifiers in gct to those in gene_sets
*.{chip}
rpt
Groovy Map containing metadata, at a minimum an id e.g. [ id:‘test’ ]
*.rpt:file
File containing parameter settings used
*.rpt
index_html
*index.html:file
Top level report HTML file
index.html
heat_map_corr_plot
*heat_map_corr_plot.html:file
HTML file combining heatmap and rank correlation plot
heat_map_corr_plot.html
report_tsvs_ref
*gsea_report_for_${reference}.tsv:file
Main TSV results report file for the reference group.
gsea_report_for_reference*.tsv
report_htmls_ref
*gsea_report_for_${reference}.html:file
Main HTML results report file for the reference group. sample groups
gsea_report_for_reference*.html
report_tsvs_target
*gsea_report_for_${target}.tsv:file
Main TSV results report file for the target group.
gsea_report_for_target*.tsv
report_htmls_target
*gsea_report_for_${target}.html:file
Main HTML results report file for the target group.
gsea_report_for_target*.html
ranked_gene_list
*ranked_gene_list*.tsv:file
TSV file with ranked gene list and scores
ranked_gene_list*.tsv
gene_set_sizes
*gene_set_sizes.tsv:file
TSV file with gene set sizes
gene_set_sizes.tsv
histogram
*global_es_histogram.png:file
Plot showing number of gene sets by enrichment score
global_es_histogram.png
heatmap
*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
*pvalues_vs_nes_plot.png:file
Plot showing FDR q-value by normalised enrichment score
ues_vs_nes_plot:file
ranked_list_corr
*ranked_list_corr_2.png:file
Ranked Gene List Correlation Profile
ranked_list_corr_2.png
butterfly_plot
*butterfly_plot.png:file
Butterfly plot with gene rank plotted against score
butterfly_plot.png
gene_set_tsv
gene_sets_*.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_sets_*.tsv
gene_set_html
gene_sets_*.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
gene_sets_*.html
gene_set_heatmap
gene_sets_*.png:list
Where -make_sets is not set to false, PNG-format heatmaps, one file for each gene set, showing expression for each gene
gene_sets_*.png
snapshot
*_snapshot*.html:list
HTML files, one each for positive and negative enrichment, collecting elements of gene_set_enplot
*_snapshot*.html
gene_set_enplot
*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
*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
*.zip:file
Where -zip_report is set, a zip archive containing all outputs
*.zip
versions
versions.yml:file
File containing software versions
versions.yml
Gene Set Enrichment Analysis (GSEA)
