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GenomicScores

Infrastructure to work with genomewide position-specific scores


Bioconductor version: Release (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")

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 2.14.3
In Bioconductor since BioC 3.5 (R-3.4) (7 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
System Requirements
URL https://github.com/rcastelo/GenomicScores
Bug Reports https://github.com/rcastelo/GenomicScores/issues
See More
Suggests RUnit, BiocStyle, knitr, rmarkdown, VariantAnnotation, gwascat, RColorBrewer, shiny, shinyjs, shinycustomloader, data.table, DT, magrittr, shinydashboard, BSgenome.Hsapiens.UCSC.hg38, phastCons100way.UCSC.hg38, MafDb.1Kgenomes.phase1.hs37d5, MafH5.gnomAD.v3.1.2.GRCh38, SNPlocs.Hsapiens.dbSNP144.GRCh37, TxDb.Hsapiens.UCSC.hg38.knownGene
Linking To
Enhances
Depends On Me AlphaMissense.v2023.hg19, AlphaMissense.v2023.hg38, cadd.v1.6.hg19, cadd.v1.6.hg38, 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.v3.1.2.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 Build Report

Package Archives

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

Source Package GenomicScores_2.14.3.tar.gz
Windows Binary GenomicScores_2.14.3.zip (64-bit only)
macOS Binary (x86_64) GenomicScores_2.14.3.tgz
macOS Binary (arm64) GenomicScores_2.14.3.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
Old Source Packages for BioC 3.18 Source Archive