GenomicFiles
This is the released version of GenomicFiles; for the devel version, see GenomicFiles.
Distributed computing by file or by range
Bioconductor version: Release (3.23)
This package provides infrastructure for parallel computations distributed 'by file' or 'by range'. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.
Author: Bioconductor Package Maintainer [aut, cre], Valerie Obenchain [aut], Michael Love [aut], Lori Shepherd [aut], Martin Morgan [aut], Sonali Kumari [ctb] (Converted 'GenomicFiles' vignettes from Sweave to RMarkdown / HTML.)
Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org>
citation("GenomicFiles")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomicFiles")
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("GenomicFiles")| Introduction to GenomicFiles | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| - YouTube | Video |
Details
| biocViews | Coverage, DataImport, Genetics, Infrastructure, Sequencing, Software |
| Version | 1.48.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (12.5 years) |
| License | Artistic-2.0 |
| Depends | BiocGenerics, BiocParallel, GenomicRanges, MatrixGenerics, methods, Rsamtools(>= 2.25.1), rtracklayer(>= 1.69.1), SummarizedExperiment(>= 1.39.1) |
| Imports | BiocBaseUtils, GenomeInfoDb(>= 1.45.7), GenomicAlignments(>= 1.45.1), IRanges, S4Vectors, Seqinfo, VariantAnnotation(>= 1.55.1) |
| System Requirements | |
| URL | https://github.com/Bioconductor/GenomicFiles |
| Bug Reports | https://github.com/Bioconductor/GenomicFiles/issues |
See More
| Suggests | BiocStyle, Biostrings, deepSNV, genefilter, Homo.sapiens, knitr, RNAseqData.HNRNPC.bam.chr14, RUnit, snpStats |
| Linking To | |
| Enhances | |
| Depends On Me | IntEREst |
| Imports Me | CAGEfightR, derfinder, gDNAx, QuasR, Rqc, TFutils, VCFArray |
| Suggests Me | ldblock, MungeSumstats |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | GenomicFiles_1.48.0.tar.gz |
| Windows Binary (x86_64) | GenomicFiles_1.48.0.zip |
| macOS Binary (big-sur-x86_64) | GenomicFiles_1.48.0.tgz |
| macOS Binary (sonoma-arm64) | GenomicFiles_1.48.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/GenomicFiles |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/GenomicFiles |
| Bioc Package Browser | https://code.bioconductor.org/browse/GenomicFiles/ |
| Package Short Url | https://bioconductor.org/packages/GenomicFiles/ |
| Package Downloads Report | Download Stats |