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
CL file with the classes of the samples in the GCT file
gene_sets
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 indicating which of the classes in the cls file should be used as the target level of the comparison.
meta2
Groovy map
chip
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 containing parameter settings used
index_html
*index.html
Top level report HTML file
index.html
heat_map_corr_plot
*heat_map_corr_plot.html
HTML file combining heatmap and rank correlation plot
heat_map_corr_plot.html
report_tsvs_ref
*gsea_report_for_${reference}.tsv
Main TSV results report file for the reference group.
gsea_report_for_reference*.tsv
report_htmls_ref
*gsea_report_for_${reference}.html
Main HTML results report file for the reference group. sample groups
gsea_report_for_reference*.html
report_tsvs_target
*gsea_report_for_${target}.tsv
Main TSV results report file for the target group.
gsea_report_for_target*.tsv
report_htmls_target
*gsea_report_for_${target}.html
Main HTML results report file for the target group.
gsea_report_for_target*.html
ranked_gene_list
*ranked_gene_list*.tsv
TSV file with ranked gene list and scores
ranked_gene_list*.tsv
gene_set_sizes
*gene_set_sizes.tsv
TSV file with gene set sizes
gene_set_sizes.tsv
histogram
*global_es_histogram.png
Plot showing number of gene sets by enrichment score
global_es_histogram.png
heatmap
*heat_map_1.png
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
Plot showing FDR q-value by normalised enrichment score
ranked_list_corr
*ranked_list_corr_2.png
Ranked Gene List Correlation Profile
ranked_list_corr_2.png
butterfly_plot
*butterfly_plot.png
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_set_html
gene_sets_*.html
Where -make_sets is not set to false, HTML files, one file for each gene set, with detail on enrichment for each gene
gene_set_heatmap
gene_sets_*.png
Where -make_sets is not set to false, PNG-format heatmaps, one file for each gene set, showing expression for each gene
snapshot
*_snapshot*.html
HTML files, one each for positive and negative enrichment, collecting elements of gene_set_enplot
gene_set_enplot
*enplot*.png
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
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
Where -zip_report is set, a zip archive containing all outputs
versions
versions.yml
File containing software versions
Gene Set Enrichment Analysis (GSEA)
