FisHiCal-package:
Iterative FISH-based Calibration of Hi-C Data
Description
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.
Details
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Package: |
| FisHiCal |
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Type: |
| Package |
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Version: |
| 1.1 |
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Date: |
| 2014-06-20 |
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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.
References
Y. Shavit, F.K. Hamey, P. Lio', FisHiCal: an R package for iterative FISH-based calibration of Hi-C data, 2014 (submitted).