gsea : Python Modules for Gene Set Enrichment Analysis

gsea current release: gsea 1.0.0

Wiki page moved to GitHub.

Requirement

• numpy Base N-dimensional array package
• scipy Fundamental library for scientific computing
• pandas Data structures & analysis
• argparse (required if Python2.6 is used)

Tested on

• Python 2.6.* (64-bit)
• Python 2.7.* (64-bit)
• CentOS 6.4
• Fedora 17
• RedHat 5.5
• Ubuntu 12.04 (python-dev and libpng-dev are required)

From source:

>>> easy_install --editable  --build-directory . ngslib
>>> cd ngslib
>>> python setup.py install

Major modules

• IO: Read various biological data
• DB: Build DB for genomic data for fast query.
• Pipeline: Pipelines built using wrappers of commonly used tools.
• Bed: Genomic coordinates data format.
• BedList: A list of Bed instances.
• TwoBitFile: python module for retrieve fasta sequence from 2bit file.
• BigWigFile: python module for retrieve Wiggle region from BigWig file.
• mFile: uniform interface for input types including regular file, sys.stdin/stdout and StringFile.

Usage

>>> import ngslib >>> for tbed in ngslib.IO.BioReader('test.bed','bed'): print tbed

>>> bwf = ngslib.DB('test.bw','bigwig') >>> for wig in bwf.fetch('chr1',1000,2000): print wig >>> depth = bwf.pileup('chr1',3000,4000) >>> bwf.close()

License

This program is released under GPLv3 license, see LICENSE for more detail.