chromoR: Analysis of chromosomal interactions data (correction, segmentation and comparison)
Version 1.0

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.

AuthorYoli Shavit
Date of publication2014-02-11 17:34:44
MaintainerYoli Shavit <ys388@cam.ac.uk>
LicenseGPL
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("chromoR")

Getting started

Package overview

Popular man pages

chromoR-package: Analysis of chromosomal interactions data (Hi-C data)
compareCIM: Compares 2 CIMs
correctCIM: Corrects a chromosomal interactions map (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...
seg: A segmentation for imr90.1 and imr90.2 CIMs
seg.imr90.obs: A segmentation for imr90.1.obs CIM
See all...

All man pages Function index File listing

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)

Functions

buildCIM Man page Source code
calcAIC Source code
calcBFMatrix Source code
chft Source code
chromoR Man page
chromoR-package Man page
cht Source code
combineToSingleMatrix Source code
compareCIM Man page Source code
convolveIter Source code
correctCIM Man page Source code
correctData Source code
correctPairCIM Man page Source code
expandMatrix Source code
fillMatrix Source code
findChangePointsForLevel Source code
findOptimalPositionWithScaleConstriant Source code
findOptimizedCP Source code
findScaleConfidenceRange Source code
findSigPosScale Source code
findWaveletMaximaByScale Source code
getOverlap Source code
imr90.1 Man page
imr90.1.obs Man page
imr90.2 Man page
matrixToVec Source code
myConv Source code
padding Source code
preprocessMaxima Source code
seg Man page
seg.imr90.obs Man page
segmentCIM Man page Source code
shiftWaveletCoeff Source code

Files

exec
exec/parse_hic_to_matrix.py
NAMESPACE
data
data/imr90.1.rda
data/imr90.2.rda
data/seg.imr90.obs.rda
data/seg.rda
data/datalist
data/imr90.1.obs.rda
R
R/HicDetect.R
R/WaveletChangePoint.R
R/buildContactMatrices.R
R/VarianceStabCorrection.R
MD5
DESCRIPTION
man
man/buildCIM.Rd
man/chromoR-package.Rd
man/compareCIM.Rd
man/imr90.1.Rd
man/imr90.1.obs.Rd
man/seg.Rd
man/correctCIM.Rd
man/imr90.2.Rd
man/seg.imr90.obs.Rd
man/segmentCIM.Rd
man/correctPairCIM.Rd
chromoR documentation built on May 20, 2017, 2:48 a.m.

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