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zqfang committed Oct 20, 2023
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Expand Up @@ -57,7 +57,7 @@ GSEApy has six sub-commands available: ``gsea``, ``prerank``, ``ssgsea``, ``repl
:gsea: The ``gsea`` module produces `GSEA <http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page>`_ results. The input requries a txt file(FPKM, Expected Counts, TPM, et.al), a cls file, and gene_sets file in gmt format.
:prerank: The ``prerank`` module produces **Prerank tool** results. The input expects a pre-ranked gene list dataset with correlation values, provided in .rnk format, and gene_sets file in gmt format. ``prerank`` module is an API to `GSEA` pre-rank tools.
:ssgsea: The ``ssgsea`` module performs **single sample GSEA(ssGSEA)** analysis. The input expects a pd.Series (indexed by gene name), or a pd.DataFrame (include ``GCT`` file) with expression values and a ``GMT`` file. For multiple sample input, ssGSEA reconigzes gct format, too. ssGSEA enrichment score for the gene set is described by `D. Barbie et al 2009 <http://www.nature.com/nature/journal/v462/n7269/abs/nature08460.html>`_.
:gsva: The ``gsva`` module performs `GSVA <https://github.com/rcastelo/GSVA>` method. The input is same to ssgsea.
:gsva: The ``gsva`` module performs `GSVA <https://github.com/rcastelo/GSVA>`_ method. The input is same to ssgsea.
:replot: The ``replot`` module reproduce GSEA desktop version results. The only input for GSEApy is the location to ``GSEA`` Desktop output results.
:enrichr: The ``enrichr`` module enable you perform gene set enrichment analysis using ``Enrichr`` API. Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr . It runs very fast.
:biomart: The ``biomart`` module helps you convert gene ids using BioMart API.
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