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 (3.21)
Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.
Author: Robert Castelo [aut, cre], Pau Puigdevall [ctb], Pablo RodrÃguez [ctb]
Maintainer: Robert Castelo <robert.castelo at upf.edu>
Citation (from within R, enter
citation("GenomicScores")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("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")| An introduction to the GenomicScores package | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, AnnotationHubSoftware, Coverage, Genetics, Infrastructure, Sequencing, Software |
| Version | 2.19.0 |
| In Bioconductor since | BioC 3.5 (R-3.4) (7.5 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, 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.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 | ATACseqQC, RareVariantVis, VariantFiltering, appreci8R, primirTSS |
| 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_2.19.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |