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Bioconductor - GenomicState

GenomicState

This is the released version of GenomicState; for the devel version, see GenomicState.

Build and access GenomicState objects for use with derfinder tools from sources like Gencode

Bioconductor version: Release (3.21)

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] ORCID: 0000-0003-2140-308X

Maintainer: Leonardo Collado-Torres <lcolladotor at gmail.com>

Citation (from within R, enter citation("GenomicState")): Installation

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


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

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")
Details biocViews AnnotationData, AnnotationHub, Homo_sapiens, TxDb Version 0.99.16 License Artistic-2.0 Depends AnnotationHub Imports GenomicFeatures, GenomeInfoDb, 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, 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.

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