Package: alabaster.files 1.3.0

Aaron Lun

alabaster.files: Wrappers to Save Common File Formats

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.

Authors:Aaron Lun [aut, cre]

alabaster.files_1.3.0.tar.gz
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alabaster.files.pdf |alabaster.files.html✨
alabaster.files/json (API)

# Install 'alabaster.files' in R:

install.packages('alabaster.files', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:alabaster.files-1.3.0(bioc 3.20)alabaster.files-1.2.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

50 exports 0.49 score 39 dependencies

Last updated 2 months agofrom:ba2759d49d

Exports:BamFileReference BamIndexWrapper BamWrapper BcfFileReference BedFileReference BedWrapper BgzipIndexWrapper BigBedFileReference BigBedWrapper BigWigFileReference BigWigWrapper compression FaIndexWrapper FastaFileReference FastaWrapper FastqFileReference FastqWrapper GffFileReference GffWrapper GmtFileReference GmtWrapper index loadBamIndexWrapper loadBamWrapper loadBedWrapper loadBgzipIndexWrapper loadBigBedWrapper loadBigWigWrapper loadFaIndexWrapper loadFastaWrapper loadFastqWrapper loadGffWrapper loadGmtWrapper loadTabixIndexWrapper loadVcfWrapper path readBamFileReference readBcfFileReference readBedFileReference readBigBedFileReference readBigWigFileReference readFastaFileReference readFastqFileReference readGffFileReference readGmtFileReference saveObject show stageObject TabixIndexWrapper VcfWrapper

Dependencies:alabaster.base alabaster.schemas askpass BH BiocGenerics BiocParallel Biostrings bitops codetools cpp11 crayon curl formatR futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicRanges httr IRanges jsonlite jsonvalidate lambda.r mime openssl R6 Rcpp rhdf5 rhdf5filters Rhdf5lib Rhtslib Rsamtools S4Vectors snow sys UCSC.utils V8 XVector zlibbioc

Saving common bioinformatics file formats

Aaron Lun

Rendered fromuserguide.Rmdusingknitr::rmarkdownon Jun 23 2024.

Last update: 2023-12-31
Started: 2023-05-02

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Reference to a BAM file	BamFileReference BamFileReference-class BamIndexWrapper BamIndexWrapper-class BamWrapper BamWrapper-class loadBamIndexWrapper loadBamWrapper readBamFileReference saveObject,BamFileReference-method stageObject,BamIndexWrapper-method stageObject,BamWrapper-method
Reference to a BCF file	BcfFileReference BcfFileReference-class loadVcfWrapper readBcfFileReference saveObject,BcfFileReference-method stageObject,VcfWrapper-method VcfWrapper VcfWrapper-class
Reference to a BED file	BedFileReference BedFileReference-class BedWrapper BedWrapper-class loadBedWrapper readBedFileReference saveObject,BedFileReference-method stageObject,BedWrapper-method
Wrapper for a Bgzip index file	BgzipIndexWrapper BgzipIndexWrapper-class loadBgzipIndexWrapper stageObject,BgzipIndexWrapper-method
Reference to a bigBed file	BigBedFileReference BigBedFileReference-class BigBedWrapper BigBedWrapper-class loadBigBedWrapper readBigBedFileReference saveObject,BigBedFileReference-method stageObject,BigBedWrapper-method
Reference to a bigWig file	BigWigFileReference BigWigFileReference-class BigWigWrapper BigWigWrapper-class loadBigWigWrapper readBigWigFileReference saveObject,BigWigFileReference-method stageObject,BigWigWrapper-method
Reference to a FASTA file	FaIndexWrapper FaIndexWrapper-class FastaFileReference FastaFileReference-class FastaWrapper FastaWrapper-class loadFaIndexWrapper loadFastaWrapper readFastaFileReference saveObject,FastaFileReference-method show,FastaWrapper-method stageObject,FaIndexWrapper-method stageObject,FastaWrapper-method
Reference to a FASTQ file	FastqFileReference FastqFileReference-class FastqWrapper FastqWrapper-class loadFastqWrapper readFastqFileReference saveObject,FastqFileReference-method show,FastqWrapper-method stageObject,FastqWrapper-method
Virtual file reference class	$,FileReference-method $<-,FileReference-method FileReference FileReference-class path,FileReference-method show,FileReference-method [[,FileReference-method [[<-,FileReference-method
Reference to a GFF file	GffFileReference GffFileReference-class GffWrapper GffWrapper-class loadGffWrapper readGffFileReference saveObject,GffFileReference-method stageObject,GffWrapper-method
Reference to a GMT file	GmtFileReference GmtFileReference-class GmtWrapper GmtWrapper-class loadGmtWrapper readGmtFileReference saveObject,GmtFileReference-method stageObject,GmtWrapper-method
Wrapper for a Tabix file	loadTabixIndexWrapper stageObject,TabixIndexWrapper-method TabixIndexWrapper TabixIndexWrapper-class
Virtual wrapper classes	CompressedIndexedWrapper-class CompressedWrapper-class compression index index,IndexedWrapper-method IndexedWrapper-class path path,Wrapper-method show,CompressedIndexedWrapper-method show,CompressedWrapper-method show,IndexedWrapper-method show,Wrapper-method virtual-wrapper Wrapper-class