chromhmmData
This is the development version of chromhmmData; for the stable release version, see chromhmmData.
Chromosome Size, Coordinates and Anchor Files
Bioconductor version: Development (3.24)
Annotation files of the formatted genomic annotation for ChromHMM. Three types of text files are included the chromosome sizes, region coordinates and anchors specifying the transcription start and end sites. The package includes data for two versions of the genome of humans and mice.
Author: Mahmoud Ahmed [aut, cre]
Maintainer: Mahmoud Ahmed <mahmoud.s.fahmy at students.kasralainy.edu.eg>
citation("chromhmmData")):
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("chromhmmData")
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("chromhmmData")| chromhmmData | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | AnnotationData, Homo_sapiens, Mus_musculus |
| Version | 0.99.2 |
| License | GPL-3 |
| Depends | R (>= 4.1) |
| Imports | |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/MahShaaban/chromhmmData/issues |
See More
| Suggests | rmarkdown, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | segmenter |
| Suggests Me | |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | chromhmmData_0.99.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Package Short Url | https://bioconductor.org/packages/chromhmmData/ |
| Package Downloads Report | Download Stats |