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

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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.

Author
Yoli Shavit
Date of publication
2014-02-11 17:34:44
Maintainer
Yoli Shavit <ys388@cam.ac.uk>
License
GPL
Version
1.0

View on CRAN

Man pages

buildCIM
Builds Chromosomal Interactions Maps
chromoR-package
Analysis of chromosomal interactions data (Hi-C data)
compareCIM
Compares 2 CIMs
correctCIM
Corrects a chromosomal interactions map (CIM)
correctPairCIM
Corrects a pairwise CIM
imr90.1
A corrected CIM of replicate 1 of IMR90, for chromosomes 1...
imr90.1.obs
A non-corrected CIM of replicate 1 of IMR90, for chromosomes...
imr90.2
A CIM of replicate 2 of IMR90, for chromosomes 1 and 2
seg
A segmentation for imr90.1 and imr90.2 CIMs
seg.imr90.obs
A segmentation for imr90.1.obs CIM
segmentCIM
Segments a 1D contact profile (1D CIM)

Files in this package

chromoR
chromoR/exec
chromoR/exec/parse_hic_to_matrix.py
chromoR/NAMESPACE
chromoR/data
chromoR/data/imr90.1.rda
chromoR/data/imr90.2.rda
chromoR/data/seg.imr90.obs.rda
chromoR/data/seg.rda
chromoR/data/datalist
chromoR/data/imr90.1.obs.rda
chromoR/R
chromoR/R/HicDetect.R
chromoR/R/WaveletChangePoint.R
chromoR/R/buildContactMatrices.R
chromoR/R/VarianceStabCorrection.R
chromoR/MD5
chromoR/DESCRIPTION
chromoR/man
chromoR/man/buildCIM.Rd
chromoR/man/chromoR-package.Rd
chromoR/man/compareCIM.Rd
chromoR/man/imr90.1.Rd
chromoR/man/imr90.1.obs.Rd
chromoR/man/seg.Rd
chromoR/man/correctCIM.Rd
chromoR/man/imr90.2.Rd
chromoR/man/seg.imr90.obs.Rd
chromoR/man/segmentCIM.Rd
chromoR/man/correctPairCIM.Rd