GenomicScores
Infrastructure to work with genomewide position-specific scores
Bioconductor version: 3.23 · Package version: 2.24.0
Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomicScores")Details
| Maintainer | Robert Castelo <robert.castelo@upf.edu> |
| Author | Robert Castelo [aut, cre], Pau Puigdevall [ctb], Pablo RodrÃguez [ctb] |
| License | Artistic-2.0 |
| URL | https://github.com/rcastelo/GenomicScores |
| Bug Reports | https://github.com/rcastelo/GenomicScores/issues |
| Downloads rank | 926 |
| Source branch | RELEASE_3_23 |
| biocViews | Annotation, AnnotationHubSoftware, Coverage, Genetics, Infrastructure, Sequencing, Software |
Documentation
Download
Dependencies
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
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
Reverse dependencies
Depends On Me (26): 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 (5): appreci8R, ATACseqQC, primirTSS, RareVariantVis, VariantFiltering
Suggests Me (1): methrix