Package: BiocIO 1.17.0

Marcel Ramos

BiocIO: Standard Input and Output for Bioconductor Packages

The `BiocIO` package contains high-level abstract classes and generics used by developers to build IO funcionality within the Bioconductor suite of packages. Implements `import()` and `export()` standard generics for importing and exporting biological data formats. `import()` supports whole-file as well as chunk-wise iterative import. The `import()` interface optionally provides a standard mechanism for 'lazy' access via `filter()` (on row or element-like components of the file resource), `select()` (on column-like components of the file resource) and `collect()`. The `import()` interface optionally provides transparent access to remote (e.g. via https) as well as local access. Developers can register a file extension, e.g., `.loom` for dispatch from character-based URIs to specific `import()` / `export()` methods based on classes representing file types, e.g., `LoomFile()`.

Authors:Martin Morgan [aut], Michael Lawrence [aut], Daniel Van Twisk [aut], Marcel Ramos [cre]

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NEWS

# Install 'BiocIO' in R:
install.packages('BiocIO', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/bioconductor/biocio/issues

On BioConductor:BiocIO-1.15.2(bioc 3.20)BiocIO-1.14.0(bioc 3.19)

annotationdataimportbioconductor-packagecore-package

10.05 score 1 stars 490 packages 16 scripts 31k downloads 10 exports 2 dependencies

Last updated 22 days agofrom:469b628afb. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winOKOct 30 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:BiocFileListdecompressexportFileForFormatfileFormatimportpathresourceresource<-show

Dependencies:BiocGenericsS4Vectors

An Overview of the BiocIO package

Rendered fromBiocIO.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2023-01-18
Started: 2020-06-01

Readme and manuals

Help Manual

Help pageTopics
BiocFile class objectsas.character,BiocFile-method BiocFile BiocFile-class BiocFileList BiocFileList-class FileForFormat fileFormat fileFormat,BiocFile-method fileFormat,character-method path path,BiocFile-method resource resource,BiocFile-method resource<- resource<-,BiocFile,character_OR_connection-method show,BiocFile-method
File compressioncompress CompressedFile-class compression decompress decompress,ANY-method decompress,character-method decompress,CompressedFile-method decompress,GZFile-method fileFormat,CompressedFile-method
Import and exportexport export,ANY,character,character-method export,ANY,character,missing-method export,ANY,CompressedFile,missing-method export,ANY,connection,character-method export,ANY,connection,missing-method export,ANY,missing,character-method import import,character,character,ANY-method import,character,missing,ANY-method import,CompressedFile,missing,ANY-method import,connection,character,ANY-method import,connection,missing,ANY-method import,missing,ANY,character-method IO