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GenomicState

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

Bioconductor version: 3.23 · Package version: 0.99.17

This package contains functions for building GenomicState objects from different annotation sources such as Gencode. It also provides access to these files at JHPCE.

Installation

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

BiocManager::install("GenomicState")

Details

MaintainerLeonardo Collado-Torres <lcolladotor@gmail.com>
AuthorLeonardo Collado-Torres [aut, cre] (ORCID: <https://orcid.org/0000-0003-2140-308X>)
LicenseArtistic-2.0
URLhttps://github.com/LieberInstitute/GenomicState
Bug Reportshttps://support.bioconductor.org/t/GenomicState
Downloads rank105
Source branchRELEASE_3_23
biocViewsAnnotationData, AnnotationHub, Homo_sapiens, TxDb

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Dependencies

Depends: AnnotationHub

Imports: Seqinfo, GenomicFeatures, rtracklayer, bumphunter, derfinder (>= 1.21.7), AnnotationDbi, IRanges, org.Hs.eg.db, utils, methods, txdbmaker

Suggests: knitr, rmarkdown, BiocStyle, sessioninfo, testthat (>= 2.1.0), glue, derfinderPlot, AnnotationHubData, GenomeInfoDbData, RefManageR, GenomicRanges, covr

Reverse dependencies

Imports Me (1): recountWorkflow