Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
1 of 6 committers (16.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.8%) to scientific vocabulary
Keywords
Keywords from Contributors
Repository
:books: R interface to the Bio-Formats library
Basic Info
- Host: GitHub
- Owner: aoles
- Language: R
- Default Branch: devel
- Homepage: https://bioconductor.org/packages/RBioFormats
- Size: 118 MB
Statistics
- Stars: 25
- Watchers: 10
- Forks: 14
- Open Issues: 21
- Releases: 0
Topics
Metadata Files
README.md
R interface to Bio-Formats
RBioFormats is an R package which provides an interface to the OME Bio-Formats Java library. It facilitates reading of proprietary image data and metadata in R.
Installation
First, make sure you have JDK 1.8 or higher installed.
To install RBioFormats use the biocLite installation script in order to resolve the dependency on the Bioconductor package EBImage.
r
if (!require("BiocManager", quietly=TRUE)) install.packages("BiocManager")
BiocManager::install("aoles/RBioFormats")
Mac OS X
Mac OS comes with a legacy Apple Java 6. In order to use RBioFormats, you will need to update your Java installation to a newer version provided by Oracle.
Install Oracle JDK.
Update R Java configuration by executing from the command line (you might have to run it as a super user by prepending
sudodepending on your installation).R CMD javareconfRe-install rJava from sources in order to properly link to the non-system Java installation.
r install.packages("rJava", type="source")
You can verify your configuration by running the following commands. This should return the Java version string corresponding to the one downloaded and installed in step 1.
```r library(rJava) .jinit() .jcall("java/lang/System", "S", "getProperty", "java.runtime.version")
[1] "1.8.0_112-b16"
```
Documentation
To get started with using RBioFormats have a look at the package vignette.
FAQ
See my answers on Stack Overflow for solutions to some common and less common questions.
Caveats
The java.lang.OutOfMemoryError error
If you get the java.lang.OutOfMemoryError: Java heap space error, try increasing the maximum heap size by supplying the -Xmx parameter before the Java Virtual Machine is initialized. For example, use
r
options( java.parameters = "-Xmx4g" )
library( "RBioFormats" )
to override the default setting and assign 4 gigabytes of heap space to the Java environment.
Information about the current Java heap space limit can be retrieved by checkJavaMemory().
Use with BiocParallel
Each R process needs a separate JVM instance. For this, load the package in the parallelized function, e.g.,
r
bplapply (files, function(f) {
library(RBioFormats)
...
})
Owner
- Name: Andrzej K. Oleś
- Login: aoles
- Kind: user
- Location: Heidelberg, Germany
- Company: @GIScience, @Bioconductor
- Twitter: andrzejkoles
- Repositories: 59
- Profile: https://github.com/aoles
Research Software Developer
GitHub Events
Total
- Issues event: 2
- Watch event: 1
- Issue comment event: 5
- Fork event: 1
Last Year
- Issues event: 2
- Watch event: 1
- Issue comment event: 5
- Fork event: 1
Committers
Last synced: over 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| aoles | a****s@g****m | 162 |
| J Wokaty | j****y | 4 |
| J Wokaty | j****y@s****u | 2 |
| Peter Hickey | p****y@g****m | 1 |
| john lee | j****h@g****m | 1 |
| john lee | l****3@q****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 39
- Total pull requests: 6
- Average time to close issues: 2 months
- Average time to close pull requests: about 2 months
- Total issue authors: 28
- Total pull request authors: 4
- Average comments per issue: 2.82
- Average comments per pull request: 1.5
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 5
- Pull requests: 0
- Average time to close issues: about 23 hours
- Average time to close pull requests: N/A
- Issue authors: 4
- Pull request authors: 0
- Average comments per issue: 1.4
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jkh1 (4)
- lambdamoses (4)
- gvogler (3)
- beansprout88 (2)
- mirickmi (2)
- aoles (2)
- kbarreto (1)
- youkefan18 (1)
- joshmoore (1)
- nalm9 (1)
- gitdemont (1)
- stetner (1)
- ajay-bhargava (1)
- TY-Cheng (1)
- QuinceyLv (1)
Pull Request Authors
- aoles (2)
- PeteHaitch (2)
- leej3 (2)
- muschellij2 (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 10,782 total
- Total dependent packages: 1
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: RBioFormats
R interface to Bio-Formats
- Homepage: https://github.com/aoles/RBioFormats
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/RBioFormats/inst/doc/RBioFormats.pdf
- License: GPL-3
-
Latest release: 1.8.0
published 9 months ago
Rankings
Maintainers (1)
Dependencies
- rJava >= 0.9 depends
- EBImage * imports
- methods * imports
- stats * imports
- BiocStyle * suggests
- XML * suggests
- knitr * suggests
- microbenchmark * suggests
- testthat * suggests