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FisHiCal (version 1.1)
Iterative FISH-based Calibration of Hi-C Data
Description
FisHiCal integrates Hi-C and FISH data, offering a modular and easy-to-use tool for chromosomal spatial analysis.
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Version
Version
1.1
1.0
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Install
install.packages('FisHiCal')
Monthly Downloads
26
Version
1.1
License
GPL
Maintainer
Yoli Shavit
Last Published
June 23rd, 2014
Functions in FisHiCal (1.1)
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calibrate
Hi-C calibration
conf
A 3D random configuration of 100 points
spatialInc
Spatial inconsistencies detected for loci in fibroblasts chromosome 1
searchInc
Search for spatial inconsistencies
prepareData
Match FISH distances and Hi-C frequencies for calibration
FisHiCal-package
Iterative FISH-based Calibration of Hi-C Data
summaryInc
Summarize spatial inconsistencies.
match
in-silico FISH distances and matching Hi-C frequencies with 5% noise
prepareCalib
Prepare Hi-C calibration
hic
in-silico 100*100 Hi-C contact matrix with with 5% noise
lsmacof
3D reconstruction from Hi-C distances
updateCalib
Update a parameter value in the calibration model
findMatchingIndices
Find matching Hi-C bins for FISH probes, using mid-points
plotInc
Plot a spatial inconsistency
calibHiC
in-silico 100*100 calibrated Hi-C contact matrix
getInfoLevelForChr
Compute the information level for a given chromosome after calibration