scHiCcompare

This is the released version of scHiCcompare; for the devel version, see scHiCcompare.

Differential Analysis of Single-cell Hi-C Data

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DOI: 10.18129/B9.bioc.scHiCcompare

Bioconductor version: Release (3.22)

This package provides functions for differential chromatin interaction analysis between two single-cell Hi-C data groups. It includes tools for imputation, normalization, and differential analysis of chromatin interactions. The package implements pooling techniques for imputation and offers methods to normalize and test for differential interactions across single-cell Hi-C datasets.

Author: My Nguyen [aut, cre] ORCID iD ORCID: 0009-0003-1118-7085 , Mikhail Dozmorov [aut] ORCID iD ORCID: 0000-0002-0086-8358

Maintainer: My Nguyen <hamy.12398 at gmail.com>

Citation (from within R, enter citation("scHiCcompare")):

Installation

To install this package, start R (version "4.5") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
BiocManager::install("scHiCcompare")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scHiCcompare")

Chromatin Differential Analysis of scHiC -scHiCcompare Vignette HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews HiC, Normalization, Sequencing, SingleCell, Software

Version 1.2.0

In Bioconductor since BioC 3.21 (R-4.5) (0.5 years)

License MIT + file LICENSE

Depends R (>= 4.5.0)

Imports grDevices, graphics, stats, utils, dplyr, ggplot2, gtools, HiCcompare, lattice, mclust, mice, miceadds, ranger, rstatix, tidyr, rlang, data.table, BiocParallel

System Requirements

URL https://github.com/dozmorovlab/ScHiCcompare

Bug Reports https://github.com/dozmorovlab/ScHiCcompare/issues

Suggests knitr, rmarkdown, testthat, BiocStyle, DT, gridExtra

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scHiCcompare_1.2.0.tar.gz

Windows Binary (x86_64) scHiCcompare_1.1.0.zip (64-bit only)

macOS Binary (x86_64) scHiCcompare_1.2.0.tgz

macOS Binary (arm64) scHiCcompare_1.2.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/scHiCcompare

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scHiCcompare

Bioc Package Browser https://code.bioconductor.org/browse/scHiCcompare/

Package Short Url https://bioconductor.org/packages/scHiCcompare/

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