run the Broad Gene Set Enrichment tool in GSEA mode
meta{:bash}
:map
Groovy Map containing metadata, at a minimum an id e.g. [ id:‘test’ ].
gct{:bash}
:file
GCT file with expression values
*.{gct}
cls{:bash}
CL file with the classes of the samples in the GCT file
gene_sets{:bash}
GMX or GMT file with gene sets
*.{gmx,gmt}
reference{:bash}
:string
String indicating which of the classes in the cls file should be used as the reference level of the comparison.
target{:bash}
String indicating which of the classes in the cls file should be used as the target level of the comparison.
meta2{:bash}
Groovy map
chip{:bash}
optional Broad-style chip file mapping identifiers in gct to those in gene_sets
*.{chip}
rpt{:bash}
Groovy Map containing metadata, at a minimum an id e.g. [ id:‘test’ ]
*.rpt{:bash}
File containing parameter settings used
*.rpt
index_html{:bash}
*index.html{:bash}
Top level report HTML file
index.html
heat_map_corr_plot{:bash}
*heat_map_corr_plot.html{:bash}
HTML file combining heatmap and rank correlation plot
heat_map_corr_plot.html
report_tsvs_ref{:bash}
*gsea_report_for_${reference}.tsv{:bash}
Main TSV results report file for the reference group.
gsea_report_for_reference*.tsv
report_htmls_ref{:bash}
*gsea_report_for_${reference}.html{:bash}
Main HTML results report file for the reference group. sample groups
gsea_report_for_reference*.html
report_tsvs_target{:bash}
*gsea_report_for_${target}.tsv{:bash}
Main TSV results report file for the target group.
gsea_report_for_target*.tsv
report_htmls_target{:bash}
*gsea_report_for_${target}.html{:bash}
Main HTML results report file for the target group.
gsea_report_for_target*.html
ranked_gene_list{:bash}
*ranked_gene_list*.tsv{:bash}
TSV file with ranked gene list and scores
ranked_gene_list*.tsv
gene_set_sizes{:bash}
*gene_set_sizes.tsv{:bash}
TSV file with gene set sizes
gene_set_sizes.tsv
histogram{:bash}
*global_es_histogram.png{:bash}
Plot showing number of gene sets by enrichment score
global_es_histogram.png
heatmap{:bash}
*heat_map_1.png{:bash}
Heat Map of the top 50 features for each phenotype in test
heat_map_1.png
pvalues_vs_nes_plot{:bash}
*pvalues_vs_nes_plot.png{:bash}
Plot showing FDR q-value by normalised enrichment score
pvalues_vs_nes_plot
ranked_list_corr{:bash}
*ranked_list_corr_2.png{:bash}
Ranked Gene List Correlation Profile
ranked_list_corr_2.png
butterfly_plot{:bash}
*butterfly_plot.png{:bash}
Butterfly plot with gene rank plotted against score
butterfly_plot.png
gene_set_tsv{:bash}
gene_sets_*.tsv{:bash}
: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{:bash}
gene_sets_*.html{:bash}
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{:bash}
gene_sets_*.png{:bash}
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{:bash}
*_snapshot*.html{:bash}
HTML files, one each for positive and negative enrichment, collecting elements of gene_set_enplot
*_snapshot*.html
gene_set_enplot{:bash}
*enplot*.png{:bash}
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{:bash}
*gset_rnd_es_dist*.png{:bash}
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{:bash}
*.zip{:bash}
Where -zip_report is set, a zip archive containing all outputs
*.zip
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
Gene Set Enrichment Analysis (GSEA)
