Description Details Author(s) References
FisHiCal is an R package for combining Hi-C and FISH data, which offers a modular and easy-to-use tool for chromosomal spatial analysis. With FisHiCal researchers can prepare and apply FISH-based Hi-C calibration, which converts contact frequencies into distances and computes a range threshold, and exploit 3D inference methods to iteratively refine it. These methods include algorithms for reconstructing chromosome structure (from calibrated distances) and for detecting spatial inconsistencies.
Package: | FisHiCal |
Type: | Package |
Version: | 1.1 |
Date: | 2014-06-20 |
License: | GPL |
FisHiCal implements the methods described in Shavit, Hamey and Lio' (2014) (submitted). Users can first prepare and apply their calibration with prepareData
, prepareCalib
and calibrate
and use 3D inference functions (lsmacof
, searchInc
, plotInc
and summaryInc
) to spatially explore their data and further refine their calibration.
Yoli Shavit, Fiona Kathryn Hamey and Pietro Lio'.
Maintainer: Yoli Shavit <ys388@cam.ac.uk>
Y. Shavit, F.K. Hamey, P. Lio', FisHiCal: an R package for iterative FISH-based calibration of Hi-C data, 2014 (submitted).
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