biomformat
Biom file format support in R/Bioconductor, vers. 1.x (JSON) and 2.x (HDF5) https://bioconductor.org/packages/release/bioc/html/biomformat.html
Science Score: 10.0%
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
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○.zenodo.json file
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○DOI references
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○Academic publication links
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✓Committers with academic emails
2 of 14 committers (14.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.3%) to scientific vocabulary
Keywords from Contributors
Repository
Biom file format support in R/Bioconductor, vers. 1.x (JSON) and 2.x (HDF5) https://bioconductor.org/packages/release/bioc/html/biomformat.html
Basic Info
- Host: GitHub
- Owner: joey711
- Language: R
- Default Branch: master
- Size: 149 KB
Statistics
- Stars: 7
- Watchers: 2
- Forks: 6
- Open Issues: 14
- Releases: 0
Metadata Files
README.md
The biomformat Package for R
About
This is an R package for interfacing with both the JSON and HDF5 versions of the biom file format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file.
Design
The design of this API is intended to match the python API where appropriate, while maintaining a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.
Installation
To install the latest stable release of the biomformat package enter the following in an R session (after official release).
S
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("biomformat")
Before official release, or to install the latest development version, enter the following into an R session.
S
install.packages("devtools") # if not already installed
devtools::install_github("joey711/biomformat")
Support
Please post feature or support requests and bugs at the Issues Tracker for the biomformat package on GitHub. Issues related to the format itself and not the R interface should be posted on the issues tracker for the biom-format team.
Note that this is a separate (but friendly!) project from the biom-format team, and the software license is different between this package and much of the rest of the biom-format software, which has switched to BSD.
This package is scheduled for inclusion in the next stable release of the Bioconductor project (BioC). BioC is also where the rhdf5 package lives.
The original release of this package was made available through CRAN, as the "biom" package, supporting version 1.x (JSON) only. The current plan is to let "biom" remain on CRAN in maintenance-only mode until "biomformat" is released on Bioconductor. At which point "biom" will be considered deprecated, and eventually removed.
Owner
- Name: Paul J. McMurdie
- Login: joey711
- Kind: user
- Location: San Francisco Bay Area, CA, USA
- Company: D2G Oncology
- Website: https://scholar.google.com/citations?hl=en&user=nNQ1LtMAAAAJ
- Twitter: joey711
- Repositories: 26
- Profile: https://github.com/joey711
Principal Bioinformatics Scientist. https://www.linkedin.com/company/d2g-oncology/about/
GitHub Events
Total
- Pull request event: 1
Last Year
- Pull request event: 1
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Nitesh Turaga | n****a@g****m | 14 |
| Dan Tenenbaum | d****a@f****g | 4 |
| Herve Pages | h****s@f****g | 4 |
| Shareef Dabdoub | s****f@d****t | 4 |
| Hervé Pagès | h****s@f****g | 2 |
| J Wokaty | j****y@s****u | 2 |
| vobencha | v****n@r****g | 2 |
| vobencha | v****a@g****m | 2 |
| J Wokaty | j****y | 2 |
| James Hester | j****r@f****g | 1 |
| Kayla-Morrell | k****l@r****g | 1 |
| LiNk-NY | m****9@g****m | 1 |
| Paul J. McMurdie | j****1@g****m | 1 |
| Paul J. McMurdie | m****e@s****u | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 12
- Total pull requests: 4
- Average time to close issues: about 1 month
- Average time to close pull requests: 10 days
- Total issue authors: 12
- Total pull request authors: 3
- Average comments per issue: 0.83
- Average comments per pull request: 1.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Midnighter (1)
- mdehollander (1)
- vebaev (1)
- gputzel (1)
- jbisanz (1)
- AgentKumara (1)
- BaxW (1)
- WaterKnight1998 (1)
- chlige (1)
- akense (1)
- sandipansamaddar (1)
- pbradz (1)
Pull Request Authors
- chlige (2)
- ycl6 (2)
- smdabdoub (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 628,746 total
- Total dependent packages: 8
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: biomformat
An interface package for the BIOM file format
- Homepage: https://github.com/joey711/biomformat/ http://biom-format.org/
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/biomformat/inst/doc/biomformat.pdf
- License: GPL-2
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Latest release: 1.36.0
published over 1 year ago