scHiCcompare

This is the development version of scHiCcompare; for the stable release version, see scHiCcompare.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21

Differential Analysis of Single-cell Hi-C Data

Bioconductor version: Development (3.24)

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: 0009-0003-1118-7085 , Mikhail Dozmorov [aut] ORCID: 0000-0002-0086-8358

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

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

My Nguyen, Mikhail Dozmorov. scHiCcompare: Differential Analysis of Single-cell Hi-C Data. doi:10.18129/B9.bioc.scHiCcompare, R package version 1.5.0, https://bioconductor.org/packages/scHiCcompare.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

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

## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")

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	1.5.0
In Bioconductor since	BioC 3.21 (R-4.5) (1.5 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
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	scHiCcompare_1.5.0.tar.gz
Windows Binary (x86_64)	scHiCcompare_1.5.0.zip
macOS Binary (big-sur-x86_64)	scHiCcompare_1.5.0.tgz
macOS Binary (sonoma-arm64)	scHiCcompare_1.5.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/scHiCcompare
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/scHiCcompare
Package Short Url	https://bioconductor.org/packages/scHiCcompare/
Package Downloads Report	Download Stats