GenomicScores

This is the development version of GenomicScores; for the stable release version, see GenomicScores.

Infrastructure to work with genomewide position-specific scores

Bioconductor version: Development (3.18)

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>

Citation (from within R, enter citation("GenomicScores")):

Installation

To install this package, start R (version "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")

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

Details

biocViews	Annotation, AnnotationHubSoftware, Coverage, Genetics, Infrastructure, Sequencing, Software
Version	2.13.0
In Bioconductor since	BioC 3.5 (R-3.4) (6.5 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
Linking To
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
System Requirements
Enhances
URL	https://github.com/rcastelo/GenomicScores
Bug Reports	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_2.13.0.tar.gz
Windows Binary	GenomicScores_2.13.0.zip
macOS Binary (x86_64)	GenomicScores_2.13.0.tgz
macOS Binary (arm64)
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