GenomicScores

DOI: 10.18129/B9.bioc.GenomicScores  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see GenomicScores.

Infrastructure to work with genomewide position-specific scores

Bioconductor version: 3.16

Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.

Author: Robert Castelo [aut, cre], Pau Puigdevall [ctb], Pablo Rodríguez [ctb]

Maintainer: Robert Castelo <robert.castelo at upf.edu>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("GenomicScores")

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("GenomicScores")

 

HTML	R Script	An introduction to the GenomicScores package
PDF		Reference Manual
Text		NEWS

Details

biocViews	Annotation, AnnotationHubSoftware, Coverage, Genetics, Infrastructure, Sequencing, Software
Version	2.10.0
In Bioconductor since	BioC 3.5 (R-3.4) (6 years)
License	Artistic-2.0
Depends	R (>= 3.5), S4Vectors(>= 0.7.21), GenomicRanges, methods, BiocGenerics(>= 0.13.8)
Imports	stats, utils, XML, httr, Biobase, BiocManager, BiocFileCache, IRanges(>= 2.3.23), Biostrings, GenomeInfoDb, AnnotationHub, rhdf5, DelayedArray, HDF5Array
LinkingTo
Suggests	RUnit, BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, phastCons100way.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5, SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation, TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard
SystemRequirements
Enhances
URL	https://github.com/rcastelo/GenomicScores
BugReports	https://github.com/rcastelo/GenomicScores/issues
Depends On Me	fitCons.UCSC.hg19, MafDb.1Kgenomes.phase1.GRCh38, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.GRCh38, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ExAC.r1.0.GRCh38, MafDb.ExAC.r1.0.hs37d5, MafDb.ExAC.r1.0.nonTCGA.GRCh38, MafDb.ExAC.r1.0.nonTCGA.hs37d5, MafDb.gnomAD.r2.1.GRCh38, MafDb.gnomAD.r2.1.hs37d5, MafDb.gnomADex.r2.1.GRCh38, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, MafH5.gnomAD.v3.1.1.GRCh38, MafH5.gnomAD.v3.1.2.GRCh38, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons30way.UCSC.hg38, phastCons35way.UCSC.mm39, phastCons7way.UCSC.hg38, phyloP35way.UCSC.mm39
Imports Me	appreci8R, ATACseqQC, primirTSS, RareVariantVis, VariantFiltering
Suggests Me	methrix
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	GenomicScores_2.10.0.tar.gz
Windows Binary	GenomicScores_2.10.0.zip (64-bit only)
macOS Binary (x86_64)	GenomicScores_2.10.0.tgz
macOS Binary (arm64)	GenomicScores_2.10.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GenomicScores
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/GenomicScores
Bioc Package Browser	https://code.bioconductor.org/browse/GenomicScores/
Package Short Url	https://bioconductor.org/packages/GenomicScores/
Package Downloads Report	Download Stats