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 (3.24)
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]
, Mikhail Dozmorov [aut]
Maintainer: My Nguyen <hamy.12398 at gmail.com>
citation("scHiCcompare")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | ||
| NEWS | Text | |
| LICENSE | Text |
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 |
See More
| Suggests | knitr, rmarkdown, testthat, BiocStyle, DT, gridExtra |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/scHiCcompare/ |
| Package Short Url | https://bioconductor.org/packages/scHiCcompare/ |
| Package Downloads Report | Download Stats |