├── .gitignore ├── CHANGES.rst ├── LICENSE ├── R ├── .Rbuildignore ├── .bumpversion.cfg ├── DESCRIPTION ├── NAMESPACE ├── R │ ├── analysis.R │ ├── background.R │ ├── data.R │ ├── grouptests.R │ ├── logspace.R │ ├── plot.R │ ├── poisbinom.R │ └── print.R ├── data │ └── BRCA.mut.RData ├── inst │ └── CITATION ├── src │ ├── Makevars │ ├── fdr.f90 │ ├── lbfgsb.f │ ├── logspace.f90 │ ├── maxent.f90 │ ├── poisbinom.f90 │ ├── rwrappers.f90 │ ├── timer.f │ ├── types.f90 │ ├── uniinv.f90 │ └── util.f90 └── vignettes │ └── discover-intro.Rmd ├── README.rst └── python ├── .bumpversion.cfg ├── conda-recipe ├── conda_build_config.yaml └── meta.yaml ├── discover.pyf ├── discover ├── __init__.py ├── background.py ├── data.py ├── datasets │ ├── __init__.py │ ├── brca_mut.npy.bz2 │ └── brca_mut.py ├── fallback │ ├── __init__.py │ └── poisbinom.py ├── grouptest.py ├── pairwise.py ├── plots.py ├── stats.py └── util.py ├── doc ├── Makefile ├── make.bat └── source │ ├── api.rst │ ├── conf.py │ ├── discover-intro.rst │ └── index.rst ├── meson.build ├── meson.options ├── pyproject.toml └── src ├── fdr.f90 ├── lbfgsb.f ├── linpack.f ├── logspace.f90 ├── maxent.f90 ├── poisbinom.f90 ├── timer.f ├── types.f90 ├── uniinv.f90 └── util.f90 /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NKI-CCB/DISCOVER/HEAD/.gitignore -------------------------------------------------------------------------------- /CHANGES.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NKI-CCB/DISCOVER/HEAD/CHANGES.rst -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NKI-CCB/DISCOVER/HEAD/LICENSE -------------------------------------------------------------------------------- /R/.Rbuildignore: 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