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chromoR (version 1.0)

Analysis of chromosomal interactions data (correction, segmentation and comparison)

Description

chromoR provides users with a statistical pipeline for analysing chromosomal interactions data (Hi-C data).It combines wavelet methods and a Bayesian approach for correction (bias and noise) and comparison (detecting significant changes between Hi-C maps) of Hi-C contact maps.In addition, it also support detection of change points in 1D Hi-C contact profiles.

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Version

Install

install.packages('chromoR')

Monthly Downloads

1

Version

1.0

License

GPL

Maintainer

Yoli Shavit

Last Published

February 11th, 2014

Functions in chromoR (1.0)

compareCIM

Compares 2 CIMs
imr90.1

A corrected CIM of replicate 1 of IMR90, for chromosomes 1 and 2
seg.imr90.obs

A segmentation for imr90.1.obs CIM
correctCIM

Corrects a chromosomal interactions map (CIM)
imr90.2

A CIM of replicate 2 of IMR90, for chromosomes 1 and 2
imr90.1.obs

A non-corrected CIM of replicate 1 of IMR90, for chromosomes 1 and 2
buildCIM

Builds Chromosomal Interactions Maps
seg

A segmentation for imr90.1 and imr90.2 CIMs
segmentCIM

Segments a 1D contact profile (1D CIM)
chromoR-package

Analysis of chromosomal interactions data (Hi-C data)
correctPairCIM

Corrects a pairwise CIM