HiCcompare
HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
Bioconductor version: 3.23 · Package version: 1.34.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust method for detecting differences between Hi-C datasets.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("HiCcompare")Details
| Maintainer | Mikhail Dozmorov <mikhail.dozmorov@gmail.com> |
| Author | Mikhail Dozmorov [aut, cre] (ORCID: <https://orcid.org/0000-0002-0086-8358>), Kellen Cresswell [aut], John Stansfield [aut] |
| License | MIT + file LICENSE |
| URL | https://github.com/dozmorovlab/HiCcompare |
| Bug Reports | https://github.com/dozmorovlab/HiCcompare/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | HiC, Normalization, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/HiCcompare/ |
Citation
From within R, enter citation("HiCcompare"):
Mikhail Dozmorov, Kellen Cresswell, John Stansfield. HiCcompare: HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets. doi:10.18129/B9.bioc.HiCcompare, R package version 1.34.0, https://bioconductor.org/packages/HiCcompare.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | HiCcompare_1.34.0.tar.gz |
| Windows binary (x86_64) | HiCcompare_1.34.0.zip |
| macOS binary (arm64) | HiCcompare_1.34.0.tgz |
| macOS binary (x86_64) | HiCcompare_1.34.0.tgz |
Dependencies
Depends: R (>= 3.5.0), dplyr
Imports: data.table, ggplot2, gridExtra, mgcv, stats, InteractionSet, GenomicRanges, IRanges, S4Vectors, BiocParallel, KernSmooth, methods, utils, graphics, pheatmap, gtools, rhdf5
Suggests: knitr, rmarkdown, testthat, multiHiCcompare
Reverse dependencies
Imports Me (4): multiHiCcompare, scHiCcompare, SpectralTAD, TADCompare