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Bioconductor - scHiCcompare (development version)

scHiCcompare

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

Differential Analysis of Single-cell Hi-C Data

Bioconductor version: Development (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: 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")): Installation

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


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

# The following initializes usage of Bioc devel
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 Details biocViews HiC, Normalization, Sequencing, SingleCell, Software Version 1.1.0 In Bioconductor since BioC 3.21 (R-4.5) (< 6 months) 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 See More Package Archives

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

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