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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

Install

install.packages('FisHiCal')

Monthly Downloads

17

Version

1.1

License

GPL

Maintainer

Yoli Shavit

Last Published

June 23rd, 2014

Functions in FisHiCal (1.1)

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