GenomicScores

DOI: 10.18129/B9.bioc.GenomicScores    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see GenomicScores.

Infrastructure to work with genomewide position-specific scores

Bioconductor version: 3.11

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 "4.0") and enter:

if (!requireNamespace("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, Coverage, Genetics, Infrastructure, Sequencing, Software
Version 2.0.0
In Bioconductor since BioC 3.5 (R-3.4) (3.5 years)
License Artistic-2.0
Depends R (>= 3.5), S4Vectors(>= 0.7.21), GenomicRanges, methods, BiocGenerics(>= 0.13.8)
Imports stats, utils, XML, Biobase, IRanges(>= 2.3.23), Biostrings, GenomeInfoDb, AnnotationHub, rhdf5, DelayedArray, HDF5Array
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, shiny, shinythemes, shinyjs, shinycustomloader, data.table, DT
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.gnomAD.r3.0.GRCh38, MafDb.gnomADex.r2.1.GRCh38, MafDb.gnomADex.r2.1.hs37d5, MafDb.TOPMed.freeze5.hg19, MafDb.TOPMed.freeze5.hg38, MafH5.gnomAD.r3.0.GRCh38, phastCons100way.UCSC.hg19, phastCons100way.UCSC.hg38, phastCons30way.UCSC.hg38, phastCons7way.UCSC.hg38
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_2.0.0.tar.gz
Windows Binary GenomicScores_2.0.0.zip
macOS 10.13 (High Sierra) GenomicScores_2.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GenomicScores
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GenomicScores
Package Short Url https://bioconductor.org/packages/GenomicScores/
Package Downloads Report Download Stats

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