FisHiCal: Iterative FISH-based Calibration of Hi-C Data

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FisHiCal integrates Hi-C and FISH data, offering a modular and easy-to-use tool for chromosomal spatial analysis.

Author
Yoli Shavit, Fiona Kathryn Hamey and Pietro Lio'
Date of publication
2014-06-24 01:22:21
Maintainer
Yoli Shavit <ys388@cam.ac.uk>
License
GPL
Version
1.1

View on CRAN

Man pages

calibHiC
in-silico 100*100 calibrated Hi-C contact matrix
calibrate
Hi-C calibration
conf
A 3D random configuration of 100 points
findMatchingIndices
Find matching Hi-C bins for FISH probes, using mid-points
FisHiCal-package
Iterative FISH-based Calibration of Hi-C Data
getInfoLevelForChr
Compute the information level for a given chromosome after...
hic
in-silico 100*100 Hi-C contact matrix with with 5% noise
lsmacof
3D reconstruction from Hi-C distances
match
in-silico FISH distances and matching Hi-C frequencies with...
plotInc
Plot a spatial inconsistency
prepareCalib
Prepare Hi-C calibration
prepareData
Match FISH distances and Hi-C frequencies for calibration
searchInc
Search for spatial inconsistencies
spatialInc
Spatial inconsistencies detected for loci in fibroblasts...
summaryInc
Summarize spatial inconsistencies.
updateCalib
Update a parameter value in the calibration model

Files in this package

FisHiCal
FisHiCal/src
FisHiCal/src/Makevars
FisHiCal/src/Makevars.win
FisHiCal/src/RcppExports.cpp
FisHiCal/src/smacof.cpp
FisHiCal/NAMESPACE
FisHiCal/data
FisHiCal/data/conf.RData
FisHiCal/data/match.RData
FisHiCal/data/spatialInc.RData
FisHiCal/data/calibHiC.RData
FisHiCal/data/datalist
FisHiCal/data/hic.RData
FisHiCal/R
FisHiCal/R/FisHiCal.R
FisHiCal/R/RcppExports.R
FisHiCal/MD5
FisHiCal/DESCRIPTION
FisHiCal/man
FisHiCal/man/conf.Rd
FisHiCal/man/lsmacof.Rd
FisHiCal/man/match.Rd
FisHiCal/man/hic.Rd
FisHiCal/man/FisHiCal-package.Rd
FisHiCal/man/searchInc.Rd
FisHiCal/man/findMatchingIndices.Rd
FisHiCal/man/getInfoLevelForChr.Rd
FisHiCal/man/calibHiC.Rd
FisHiCal/man/plotInc.Rd
FisHiCal/man/prepareData.Rd
FisHiCal/man/prepareCalib.Rd
FisHiCal/man/updateCalib.Rd
FisHiCal/man/spatialInc.Rd
FisHiCal/man/summaryInc.Rd
FisHiCal/man/calibrate.Rd