A function for reconstructing the 3D configuration from pairwise calibrated Hi-C distances through local stress minimization (see details).
● Data Source:
CranContrib
● Keywords:
● Alias: lsmacof
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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.
● Data Source:
CranContrib
● Keywords: package
● Alias: FisHiCal, FisHiCal-package
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0 images
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A function to test for spatial inconsistencies in a calibrated Hi-C distance matrix.
● Data Source:
CranContrib
● Keywords:
● Alias: searchInc
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A function for finding matching indices of Hi-C bins for FISH probes, based on the mid-points of their coordinates. Given the start and end coordinates of a set of FISH probes, the function finds the matching Hi-C bins and returns their indices in the given hicCoord data frame.
● Data Source:
CranContrib
● Keywords:
● Alias: findMatchingIndices
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A function to compute the information proportions in a a given calibrated Hi-C matrix for a given chromosome. This will be the proportions of non-zero cells, representing information that was not discarded in the calibration step.
● Data Source:
CranContrib
● Keywords:
● Alias: getInfoLevelForChr
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A function to plot a spatial inconsistency for a given loci (bin).
● Data Source:
CranContrib
● Keywords:
● Alias: plotInc
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1 images
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A function to match FISH distances and Hi-C frequencies based on matching probe/bin coordinates.
● Data Source:
CranContrib
● Keywords:
● Alias: prepareData
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A function to build a calibration function, by fitting a subset of FISH distances and Hi-C frequencies with a power law model (see details). The number of distances to fit (taking distances by increasing order) or a subset of selected distances should be provided by the user. Users can also choose how to estimate the distance threshold or may explicitly provide one.
● Data Source:
CranContrib
● Keywords:
● Alias: prepareCalib
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A function to update a given parameter in the calibration model.
● Data Source:
CranContrib
● Keywords:
● Alias: updateCalib
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A function to summarize the details of spatial inconsistencies detected with searchInc .
● Data Source:
CranContrib
● Keywords:
● Alias: summaryInc
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