DOI: 10.18129/B9.bioc.multiHiCcompare  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see multiHiCcompare.

Normalize and detect differences between Hi-C datasets when replicates of each experimental condition are available

Bioconductor version: 3.16

multiHiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. This extension of the original HiCcompare package now allows for Hi-C experiments with more than 2 groups and multiple samples per group. multiHiCcompare operates on processed Hi-C data in the form of sparse upper triangular matrices. It accepts four column (chromosome, region1, region2, IF) tab-separated text files storing chromatin interaction matrices. multiHiCcompare provides cyclic loess and fast loess (fastlo) methods adapted to jointly normalizing Hi-C data. Additionally, it provides a general linear model (GLM) framework adapting the edgeR package to detect differences in Hi-C data in a distance dependent manner.

Author: John Stansfield <stansfieldjc at>, Mikhail Dozmorov <mikhail.dozmorov at>

Maintainer: John Stansfield <stansfieldjc at>, Mikhail Dozmorov <mikhail.dozmorov at>

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biocViews HiC, Normalization, Sequencing, Software
Version 1.16.0
In Bioconductor since BioC 3.8 (R-3.5) (4.5 years)
License MIT + file LICENSE
Depends R (>= 4.0.0)
Imports data.table, dplyr, HiCcompare, edgeR, BiocParallel, qqman, pheatmap, methods, GenomicRanges, graphics, stats, utils, pbapply, GenomeInfoDbData, GenomeInfoDb, aggregation
Suggests knitr, rmarkdown, testthat, BiocStyle
Depends On Me
Imports Me HiCDOC
Suggests Me HiCcompare
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