format_from_gmt

path


Import data from gmt files
Convert gmt file to dataframe that can be used for anaysis


Compute and represent gene set enrichment or depletion from your
data based on pre-saved maps from the Atlas of Cancer Signalling Networks (ACSN)
or user imported maps. User imported maps must be complying with the GMT format
as defined by the Broad Institute, that is to say that the file should be tab-
separated, that the first column should contain the module name, the second
column can contain comments that will be overwritten with the number of genes
in the module, and subsequent columns must contain the list of genes (HUGO
symbols; tab-separated) inside the module. The gene set enrichment can be run
with hypergeometric test or Fisher exact test, and can use multiple corrections.
Visualization of data can be done either by barplots or heatmaps.

format_from_gmt: Import data from gmt files Convert gmt file to dataframe that can be used for anaysis

Description

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Examples