GenomicState
This is the development version of GenomicState; for the stable release version, see GenomicState.
Build and access GenomicState objects for use with derfinder tools from sources like Gencode
Bioconductor version: Development (3.24)
This package contains functions for building GenomicState objects from different annotation sources such as Gencode. It also provides access to these files at JHPCE.
Author: Leonardo Collado-Torres [aut, cre]
Maintainer: Leonardo Collado-Torres <lcolladotor at gmail.com>
citation("GenomicState")):
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("GenomicState")
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("GenomicState")| Introduction to GenomicState | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | AnnotationData, AnnotationHub, Homo_sapiens, TxDb |
| Version | 0.99.17 |
| License | Artistic-2.0 |
| Depends | AnnotationHub |
| Imports | Seqinfo, GenomicFeatures, rtracklayer, bumphunter, derfinder(>= 1.21.7), AnnotationDbi, IRanges, org.Hs.eg.db, utils, methods, txdbmaker |
| System Requirements | |
| URL | https://github.com/LieberInstitute/GenomicState |
| Bug Reports | https://support.bioconductor.org/t/GenomicState |
See More
| Suggests | knitr, rmarkdown, BiocStyle, sessioninfo, testthat (>= 2.1.0), glue, derfinderPlot, AnnotationHubData, GenomeInfoDbData, RefManageR, GenomicRanges, covr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | recountWorkflow |
| Suggests Me | |
| Links To Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GenomicState_0.99.17.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Package Short Url | https://bioconductor.org/packages/GenomicState/ |
| Package Downloads Report | Download Stats |