GenomicScores

DOI: 10.18129/B9.bioc.GenomicScores    

This is the development version of GenomicScores; for the stable release version, see GenomicScores.

Infrastructure to work with genomewide position-specific scores

Bioconductor version: Development (3.12)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 2.1.0
In Bioconductor since BioC 3.5 (R-3.4) (3 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
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_2.1.0.tar.gz
Windows Binary GenomicScores_2.1.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)
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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