A command-line tool and a python library that manipulates BED files of possibly irregularly spaced P-values and (1) calculates auto-correlation, (2) combines adjacent P-values, (3) performs false discovery adjustment, (4) finds regions of enrichment (i.e. series of adjacent low P-values) and (5) assigns significance to those regions. In addition, tools are provided for visualization and assessment. The comb-p software is useful in contexts where auto-correlated P-values are generated across the genome. Because the library accepts input in a simple, standardized format and is unaffected by the origin of the P-values, it can be used for a wide variety of applications.

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comb-p classification

comb-p specifications

Software type:
Package
Restrictions to use:
None
Programming languages:
Python
Computer skills:
Advanced
Requirements:
Python 2.7
Interface:
Command line interface
Operating system:
Unix/Linux
License:
MIT License
Stability:
Stable

Publications

  • (Pedersen et al., 2012) Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values. Bioinformatics.
    PMID: 22954632

comb-p support

Documentation

Maintainer

Credits

Institution(s)

Department of Medicine, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO, USA; Department of Biostatistics and Informatics, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO, USA

Funding source(s)

The National Institutes of Health (AA016922, HL101251, AI90052 and HL101715)

Link to literature

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