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docs update
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Zhuoqing Fang committed Dec 1, 2017
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2 changes: 1 addition & 1 deletion README.rst
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Expand Up @@ -47,7 +47,7 @@ GSEAPY has five sub-commands available: ``gsea``, ``prerank``, ``ssgsea``, ``rep

:gsea: The ``gsea`` module produce `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 produce **Prerank tool** results. The input expects a pre-ranked gene list dataset with correlation values, which in .rnk format, and gene_sets file in gmt format. ``prerank`` module is an API to `GSEA` pre-rank tools.
:ssgsea: The ``ssgsea`` module perform **single sample GSEA(ssGSEA)** analysis. The input expects a gene list with expression values(same format with ``.rnk`` file, and gene_sets file in gmt format. For multi sample input, ssGSEA reconigze gct format, too. ssGSEA enrichment score for the gene set as described by `D. Barbie et al 2009 <http://www.nature.com/nature/journal/v462/n7269/abs/nature08460.html>`_.
:ssgsea: The ``ssgsea`` module perform **single sample GSEA(ssGSEA)** analysis. The input expects a gene list, gct file, or dataframe with expression values(same format with ``.rnk`` file, and gene_sets file in gmt format. For multi sample input, ssGSEA reconigze gct format, too. ssGSEA enrichment score for the gene set as described by `D. Barbie et al 2009 <http://www.nature.com/nature/journal/v462/n7269/abs/nature08460.html>`_.

:replot: The ``replot`` module reproduce GSEA desktop version results. The only input for GSEAPY is the location to ``GSEA`` Desktop output results.

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3 changes: 1 addition & 2 deletions gseapy/__init__.py
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from .gsea import call, replot, prerank, gsea, ssgsea
from .enrichr import enrichr
from .parser import get_library_name

__version__='0.8.10'
from .__main__ import __version__
2 changes: 1 addition & 1 deletion gseapy/__main__.py
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# or args = argparser.parse_args() will throw bugs!!!


__version__ = '0.8.10'
__version__ = '0.8.11'

def main():
"""The Main function/pipeline for GSEAPY."""
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2 changes: 1 addition & 1 deletion setup.py
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__version__='0.8.10'
__version__='0.8.11'

if sys.argv[-1] == 'publish':
os.system("python setup.py sdist bdist_wheel register upload")
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