Science Score: 10.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
○codemeta.json file
-
○.zenodo.json file
-
○DOI references
-
○Academic publication links
-
✓Committers with academic emails
4 of 11 committers (36.4%) from academic institutions -
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (9.7%) to scientific vocabulary
Repository
Tidy up computational biology objects
Statistics
- Stars: 50
- Watchers: 10
- Forks: 12
- Open Issues: 12
- Releases: 0
Metadata Files
README.md
biobroom: Tidying up computational biology
This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same the tidy/augment/glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.
biobroom implements tidying methods for both S3 and S4 classes. Objects that can be tidied include
- ExpressionSet objects
- RangedSummarizedExperiment objects
- MSnSet objects
- per-gene differential expression tests from limma, edgeR, and DESeq2
- qvalue multiple hypothesis testing objects
Installation
The package can be installed with (requires devtools):
devtools::install_github("StoreyLab/biobroom")
Find out more about the provided methods with:
library(biobroom)
?edgeR_tidiers
?DESeq2_tidiers
?limma_tidiers
?ExpressionSet_tidiers
?MSnSet_tidiers
?GRangesList
?GRanges
?SummarizedExperiment_tidiers
Note on returned values
All biobroom tidy and augment methods, since they tend to be large data frames, return a tbl_df by default (this prevents them from printing many rows at once, while still acting like a traditional data.frame). To change this to a data.frame or data.table, you can set the biobroom.return option:
options(biobroom.return = "data.frame")
options(biobroom.return = "data.table")
Owner
- Name: Storey Lab
- Login: StoreyLab
- Kind: organization
- Location: Princeton, NJ USA
- Website: http://genomics.princeton.edu/storeylab/
- Repositories: 27
- Profile: https://github.com/StoreyLab
Storey Lab at Princeton University
GitHub Events
Total
- Watch event: 2
- Issue comment event: 1
Last Year
- Watch event: 2
- Issue comment event: 1
Committers
Last synced: about 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Andrew Bass | a****s@p****u | 78 |
| dgrtwo | d****o@p****u | 12 |
| andy | a****9@g****m | 9 |
| Andrew Bass | a****s@A****l | 6 |
| en99sy | e****n@p****u | 6 |
| Steve Lianoglou | l****e@g****m | 4 |
| Andrew Bass | a****s@A****l | 3 |
| Laurent | l****0@c****k | 3 |
| John D. Storey | j****y | 2 |
| Aaron Wolen | a****n@w****m | 1 |
| ltobalina | l****a | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 21
- Total pull requests: 7
- Average time to close issues: 3 months
- Average time to close pull requests: 2 days
- Total issue authors: 14
- Total pull request authors: 6
- Average comments per issue: 0.48
- Average comments per pull request: 0.29
- Merged pull requests: 5
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 1
- Pull request authors: 0
- Average comments per issue: 1.0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- dgrtwo (6)
- ajbass (3)
- ewallace (1)
- simonpcouch (1)
- Julia-F-S (1)
- LTLA (1)
- davidroberson (1)
- hummuscience (1)
- wanganlin00 (1)
- clairemcwhite (1)
- heike (1)
- chapmandu2 (1)
- tavareshugo (1)
- therealjpetereit (1)
Pull Request Authors
- lianos (2)
- ltobalina (1)
- llrs (1)
- MahShaaban (1)
- aaronwolen (1)
- lgatto (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 36,233 total
- Total dependent packages: 1
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: biobroom
Turn Bioconductor objects into tidy data frames
- Homepage: https://github.com/StoreyLab/biobroom
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/biobroom/inst/doc/biobroom.pdf
- License: LGPL
-
Latest release: 1.40.0
published over 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.0.0 depends
- broom * depends
- Biobase * imports
- dplyr * imports
- tidyr * imports
- DESeq2 * suggests
- GenomicRanges * suggests
- MSnbase * suggests
- SummarizedExperiment * suggests
- airway * suggests
- data.table * suggests
- edgeR * suggests
- ggplot2 * suggests
- knitr * suggests
- limma * suggests
- magrittr * suggests
- plyr * suggests
- qvalue * suggests
- testthat * suggests