GenomicScores

DOI: 10.18129/B9.bioc.GenomicScores    

Infrastructure to work with genomewide position-specific scores

Bioconductor version: Release (3.6)

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

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

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("GenomicScores")

Documentation

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

Details

biocViews	Annotation, Coverage, Genetics, Infrastructure, Sequencing, Software
Version	1.2.2
In Bioconductor since	BioC 3.5 (R-3.4) (1 year)
License	Artistic-2.0
Depends	R (>= 3.4), S4Vectors(>= 0.7.21), GenomicRanges, methods, BiocGenerics(>= 0.13.8)
Imports	utils, XML, Biobase, IRanges(>= 2.3.23), Biostrings, BSgenome, GenomeInfoDb, AnnotationHub
LinkingTo
Suggests	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
SystemRequirements
Enhances
URL	https://github.com/rcastelo/GenomicScores
BugReports	https://github.com/rcastelo/GenomicScores/issues
Depends On Me	fitCons.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5, MafDb.1Kgenomes.phase3.hs37d5, MafDb.ESP6500SI.V2.SSA137.GRCh38, MafDb.ESP6500SI.V2.SSA137.hs37d5, MafDb.ExAC.r1.0.hs37d5, MafDb.ExAC.r1.0.nonTCGA.hs37d5, MafDb.gnomAD.r2.0.1.hs37d5, MafDb.gnomADex.r2.0.1.hs37d5, MafDb.TOPMed.freeze5.hg38, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons7way.UCSC.hg38
Imports Me	ATACseqQC, RareVariantVis, VariantFiltering
Suggests Me
Build Report

Package Archives

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

Source Package	GenomicScores_1.2.2.tar.gz
Windows Binary	GenomicScores_1.2.2.zip
Mac OS X 10.11 (El Capitan)	GenomicScores_1.2.2.tgz
Source Repository	git clone https://git.bioconductor.org/packages/GenomicScores
Package Short Url	http://bioconductor.org/packages/GenomicScores/
Package Downloads Report	Download Stats
Old Source Packages for BioC 3.6	Source Archive