diff --git a/README.rst b/README.rst index 8d72c2f..dc3e611 100644 --- a/README.rst +++ b/README.rst @@ -57,7 +57,7 @@ GSEApy has 7 sub-commands available: ``gsea``, ``prerank``, ``ssgsea``, ``gsva`` :gsea: The ``gsea`` module produces `GSEA `_ 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 `_. -:gsva: The ``gsva`` module performs `GSVA `_ method. The input is same to ssgsea. +:gsva: The ``gsva`` module performs `GSVA `_ method by `Hänzelmann et al `_. 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. @@ -129,20 +129,15 @@ Dependency Mandatory ~~~~~~~~~ -build - -* Rust: For gseapy > 0.11.0, Rust compiler is needed -* setuptools-rust - -run - -* Numpy >= 1.13.0 -* Scipy -* Pandas -* Matplotlib -* Requests - - +* build + * Rust: For gseapy > 0.11.0, Rust compiler is needed + * setuptools-rust +* run + * Numpy >= 1.13.0 + * Scipy + * Pandas + * Matplotlib + * Requests Run GSEApy ----------------- @@ -167,7 +162,7 @@ For command line usage: # An example to run ssGSEA using gseapy ssgsea module $ gseapy ssgsea -d expression.txt -g gene_sets.gmt -o test - # An example to run ssGSEA using gseapy ssgsea module + # An example to run GSVA using gseapy ssgsea module $ gseapy gsva -d expression.txt -g gene_sets.gmt -o test # An example to use enrichr api @@ -216,14 +211,14 @@ see detail here: `Example