提交 626e6e30 编写于 作者: rictjo's avatar rictjo

package

上级 b4844502
init: init:
pip install -r requirements.txt pip install -r requirements.txt
# Group Factor Analysis Code # Simple Group Factor Analysis
Decomposes a set of expressions into a group expression Decomposes a set of expressions into a group expression.
and calculates how it is regulated via an ANOVA that is The expression regulation can be studied via an ANOVA that
relating it to the observables in the journal file. The relates it to the observables in the journal file. The
final p values are then fdr corrected and the resulting final p values are then FDR corrected and the resulting
q values are also calculated. q values are produced.
The journal and analyte expression file must be ordered The journal and analyte expression file must be ordered
the same way with respect to the samples that are the same way with respect to the samples that are
positioned on the columns. positioned on the columns.
Install with:
pip install --index-url https://test.pypi.org/simple/ impetuous-gfa
Visit the active code via:
https://github.com/richardtjornhammar/impetuous
Visit the published code:
https://doi.org/10.5281/zenodo.2594691
Cite using
DOI: 10.5281/zenodo.2594691
pandas==0.23.4 pandas==0.23.4
numpy==1.13.3 numpy==1.13.3
statsmodels==0.9.0 statsmodels==0.9.0
sklearn==0.19.0 scikit-learn==0.19.0
scipy==0.19.1 scipy==0.19.1
patsy==0.5.0 patsy==0.5.0
...@@ -5,7 +5,7 @@ with open("README.md", "r") as fh: ...@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
setuptools.setup( setuptools.setup(
name="impetuous-gfa", name="impetuous-gfa",
version="0.1.0", version="0.1.2",
author="Richard Tjörnhammar", author="Richard Tjörnhammar",
author_email="richard.tjornhammar@gmail.com", author_email="richard.tjornhammar@gmail.com",
description="Impetuous Group Factor Analysis", description="Impetuous Group Factor Analysis",
...@@ -15,8 +15,7 @@ setuptools.setup( ...@@ -15,8 +15,7 @@ setuptools.setup(
packages=setuptools.find_packages(), packages=setuptools.find_packages(),
classifiers=[ classifiers=[
"Programming Language :: Python :: 3", "Programming Language :: Python :: 3",
"License :: OSI Approved :: Apache License 2.0", "License :: OSI Approved :: Apache Software License",
"Operating System :: OS Independent", "Operating System :: OS Independent",
"Domain :: Group Factor Analysis",
], ],
) )
...@@ -109,5 +109,6 @@ if __name__ == '__main__' : ...@@ -109,5 +109,6 @@ if __name__ == '__main__' :
analyte_df = pd.read_csv(analyte_file,'\t' , index_col=0 ) analyte_df = pd.read_csv(analyte_file,'\t' , index_col=0 )
journal_df = prune_journal( pd.read_csv(journal_file,'\t', index_col=0 ) ) journal_df = prune_journal( pd.read_csv(journal_file,'\t', index_col=0 ) )
print ( quantify_groups( analyte_df, journal_df, 'Group ~ Var + C(Cat) ', grouping_file ) ) print ( quantify_groups( analyte_df, journal_df, 'Group ~ Var + C(Cat) ', grouping_file ) )
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