PCHiCdata
This is the released version of PCHiCdata; for the devel version, see PCHiCdata.
Promoter Capture Hi-C data
Bioconductor version: Release (3.23)
Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC.
Author: Paula Freire-Pritchett, Jonathan Cairns, Steven Wingett, Mikhail Spivakov
Maintainer: Mikhail Spivakov <mikhail.spivakov at lms.mrc.ac.uk>
citation("PCHiCdata")):
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")
BiocManager::install("PCHiCdata")
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("PCHiCdata")| PCHiCdata Vignette | HTML | R Script |
| Reference Manual |
Details
| biocViews | ExperimentData, Homo_sapiens_Data, Mus_musculus_Data, SequencingData, StemCell |
| Version | 1.40.0 |
| License | Artistic-2.0 |
| Depends | R (>= 3.2), Chicago |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | testthat, BiocStyle, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | Chicago |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | PCHiCdata_1.40.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/PCHiCdata |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PCHiCdata |
| Package Short Url | https://bioconductor.org/packages/PCHiCdata/ |
| Package Downloads Report | Download Stats |