GenomicScores

DOI: 10.18129/B9.bioc.GenomicScores  

Infrastructure to work with genomewide position-specific scores

Bioconductor version: Release (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>

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

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

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: