GenomicScores

This is thedevelopment version of GenomicScores; for the stable release version, seeGenomicScores.

Infrastructure to work with genomewide position-specific scores

DOI: 10.18129/B9.bioc.GenomicScores

Bioconductor version: Development (3.23)

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, entercitation("GenomicScores")):

Installation

To install this package, start R (version "4.6") and enter:

if (!require("BiocManager", quietly = TRUE))    install.packages("BiocManager")# The following initializes usage of Bioc develBiocManager::install(version='devel')BiocManager::install("GenomicScores")

For older versions of R, please refer to the appropriateBioconductor 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	Annotation,AnnotationHubSoftware,Coverage,Genetics,Infrastructure,Sequencing,Software
Version	2.23.0
In Bioconductor since	BioC 3.5 (R-3.4) (8.5 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,Seqinfo,GenomeInfoDb(>= 1.45.5),AnnotationHub,rhdf5,DelayedArray,HDF5Array
System Requirements
URL	https://github.com/rcastelo/GenomicScores
Bug Reports	https://github.com/rcastelo/GenomicScores/issues

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.v4.0.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.v4.0.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

FollowInstallation instructions to use this package in your R session.

Source Package	GenomicScores_2.23.0.tar.gz
Windows Binary (x86_64)	GenomicScores_2.23.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)	GenomicScores_2.23.0.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

Movatterモバイル変換

Menu