alabaster.files
This is the released version of alabaster.files; for the devel version, see alabaster.files.
Wrappers to Save Common File Formats
Bioconductor version: Release (3.23)
Save common bioinformatics file formats within the alabaster framework. This includes BAM, BED, VCF, bigWig, bigBed, FASTQ, FASTA and so on. We save and load additional metadata for each file, and we support linkage between each file and its corresponding index.
Author: Aaron Lun [aut, cre]
Maintainer: Aaron Lun <infinite.monkeys.with.keyboards at gmail.com>
citation("alabaster.files")):
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("alabaster.files")
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("alabaster.files")| Saving common file formats | HTML | R Script |
| Reference Manual | ||
| LICENSE | Text |
Details
| biocViews | DataImport, DataRepresentation, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | MIT + file LICENSE |
| Depends | alabaster.base |
| Imports | methods, S4Vectors, BiocGenerics, Rsamtools |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, rmarkdown, knitr, testthat, VariantAnnotation, rtracklayer, Biostrings |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | alabaster.files_1.10.0.tar.gz |
| Windows Binary (x86_64) | alabaster.files_1.10.0.zip |
| macOS Binary (big-sur-x86_64) | alabaster.files_1.10.0.tgz |
| macOS Binary (sonoma-arm64) | alabaster.files_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/alabaster.files |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/alabaster.files |
| Bioc Package Browser | https://code.bioconductor.org/browse/alabaster.files/ |
| Package Short Url | https://bioconductor.org/packages/alabaster.files/ |
| Package Downloads Report | Download Stats |