RBioFormats

This is the development version of RBioFormats; for the stable release version, see RBioFormats.

R interface to Bio-Formats

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DOI: 10.18129/B9.bioc.RBioFormats

Bioconductor version: Development (3.23)

An R package which interfaces the OME Bio-Formats Java library to allow reading of proprietary microscopy image data and metadata.

Author: Andrzej Oleś [aut, cre] ORCID iD ORCID: 0000-0003-0285-2787 , John Lee [ctb] ORCID iD ORCID: 0000-0001-5884-4247

Maintainer: Andrzej Oleś <andrzej.oles at gmail.com>

Citation (from within R, enter citation("RBioFormats")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("RBioFormats")

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("RBioFormats")

RBioFormats: an R interface to the Bio-Formats library HTML R Script

Reference Manual PDF

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DataImport, Software

Version 1.11.0

In Bioconductor since BioC 3.17 (R-4.3) (2.5 years)

License GPL-3

Depends

Imports EBImage, methods, rJava (>= 0.9-6), S4Vectors, stats

System Requirements Java (>= 1.7)

URL https://github.com/aoles/RBioFormats

Bug Reports https://github.com/aoles/RBioFormats/issues

Suggests BiocStyle, knitr, testthat, xml2

Linking To

Enhances

Depends On Me

Imports Me alabaster.sfe, islify, SpatialOmicsOverlay

Suggests Me SpatialFeatureExperiment, Voyager

Links To Me

Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package RBioFormats_1.11.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) RBioFormats_1.11.0.tgz

macOS Binary (arm64) RBioFormats_1.11.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/RBioFormats

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/RBioFormats

Bioc Package Browser https://code.bioconductor.org/browse/RBioFormats/

Package Short Url https://bioconductor.org/packages/RBioFormats/

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