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
2 of 30 committers (6.7%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.4%) to scientific vocabulary
Keywords
analysis
bioconductor
microbiome
Keywords from Contributors
bioinformatics
bioconductor-package
gene
illumina
proteomics
u24ca289073
annotation-agnostic
count
exon
human
Last synced: 6 months ago
·
JSON representation
Repository
Microbiome analysis
Basic Info
- Host: GitHub
- Owner: microbiome
- License: artistic-2.0
- Language: R
- Default Branch: devel
- Homepage: https://microbiome.github.io/mia/
- Size: 35.2 MB
Statistics
- Stars: 53
- Watchers: 7
- Forks: 32
- Open Issues: 32
- Releases: 0
Topics
analysis
bioconductor
microbiome
Created over 5 years ago
· Last pushed 6 months ago
Metadata Files
Readme
Changelog
Contributing
License
README.md
mia - Microbiome analysis 
Using the package
This project provides functions and workflows examples for analyses
of microbiome data. The main class for working with microbiome data in this
package is TreeSummarizedExperiment.
For examples of functionality, see the function reference page.
More information and example workflows are provided in the online manual Orchestrating Microbiome Analysis with Bioconductor.
Installation
Bioc-release
``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("mia") ```
Bioc-devel
``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("mia") ```
Contributing
Contributions are welcome in the form of feedback, issues, pull requests etc, see contributor guidelines.
Code of conduct
Please note that the mia project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.
Owner
- Name: microbiome
- Login: microbiome
- Kind: organization
- Email: microbiome-admin@googlegroups.com
- Location: Tools for microbiome analytics
- Website: microbiome.github.com
- Repositories: 35
- Profile: https://github.com/microbiome
Microbiome research methods
GitHub Events
Total
- Issues event: 84
- Watch event: 4
- Delete event: 51
- Issue comment event: 220
- Push event: 436
- Pull request review event: 63
- Pull request review comment event: 69
- Pull request event: 122
- Fork event: 5
- Create event: 60
Last Year
- Issues event: 84
- Watch event: 4
- Delete event: 51
- Issue comment event: 220
- Push event: 436
- Pull request review event: 63
- Pull request review comment event: 69
- Pull request event: 122
- Fork event: 5
- Create event: 60
Committers
Last synced: 9 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Tuomas Borman | 6****n | 225 |
| Felix Ernst | f****t@o****m | 141 |
| Leo Lahti | l****i@i****i | 43 |
| Théotime Pralas | 1****s | 30 |
| Muluh | 1****8 | 27 |
| Sudarshan | s****9@g****m | 23 |
| Tuomas Borman | 6****m | 21 |
| Giulio Benedetti | g****0@g****m | 11 |
| ake | 4****3 | 10 |
| J Wokaty | j****y@s****u | 10 |
| Nitesh Turaga | n****a@g****m | 6 |
| ChouaibB | 8****B | 4 |
| yiluheihei | y****i@g****m | 4 |
| Artur Sannikov | 4****v | 3 |
| Himmi Lindgren | 1****l | 3 |
| A Wokaty | a****y@s****u | 2 |
| BananaCancer | 7****r | 2 |
| Danielle Callan | 5****n | 2 |
| Eineje Ameh | 1****2 | 2 |
| Renuka Potbhare | 5****3 | 2 |
| jepasan | 1****n | 2 |
| nmdegunst | 7****h | 2 |
| Domenick Braccia | d****a@g****m | 2 |
| Hervé Pagès | h****b@g****m | 1 |
| Katariina Pärnänen | 3****n | 1 |
| Moritz E. Beber | m****r@p****t | 1 |
| Sam Hillman | 1****6 | 1 |
| Shadman Ishraq | 1****q | 1 |
| erawijantari | 4****i | 1 |
| shigdel | 8****l | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 174
- Total pull requests: 317
- Average time to close issues: 7 months
- Average time to close pull requests: 12 days
- Total issue authors: 28
- Total pull request authors: 23
- Average comments per issue: 4.17
- Average comments per pull request: 2.05
- Merged pull requests: 249
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 46
- Pull requests: 144
- Average time to close issues: 10 days
- Average time to close pull requests: 6 days
- Issue authors: 11
- Pull request authors: 10
- Average comments per issue: 1.17
- Average comments per pull request: 0.98
- Merged pull requests: 113
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- antagomir (85)
- TuomasBorman (34)
- artur-sannikov (10)
- RiboRings (7)
- Daenarys8 (4)
- microsud (4)
- thpralas (3)
- FelixErnst (3)
- g-antonello (2)
- nr0cinu (2)
- exod1a (2)
- xec-cm (2)
- carlosmandoz (1)
- ChouaibB (1)
- J5886 (1)
Pull Request Authors
- TuomasBorman (157)
- Daenarys8 (38)
- thpralas (32)
- FelixErnst (26)
- ake123 (12)
- RiboRings (11)
- antagomir (10)
- artur-sannikov (6)
- Insaynoah (3)
- yiluheihei (3)
- d-callan (3)
- jepasan (2)
- eotamm (2)
- microsud (2)
- AliHajj20 (2)
Top Labels
Issue Labels
enhancement (27)
question (7)
bug (4)
documentation (2)
help wanted (1)
Pull Request Labels
enhancement (2)
bug (1)
ready (1)
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 125,046 total
- Total dependent packages: 7
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: mia
Microbiome analysis
- Homepage: https://github.com/microbiome/mia
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/mia/inst/doc/mia.pdf
- License: Artistic-2.0 | file LICENSE
-
Latest release: 1.16.1
published 7 months ago
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Stargazers count: 4.2%
Forks count: 5.4%
Average: 6.7%
Downloads: 23.8%
Maintainers (1)
Last synced:
6 months ago
Dependencies
DESCRIPTION
cran
- MultiAssayExperiment * depends
- R >= 4.0 depends
- SingleCellExperiment * depends
- SummarizedExperiment * depends
- TreeSummarizedExperiment >= 1.99.3 depends
- BiocGenerics * imports
- BiocParallel * imports
- Biostrings * imports
- DECIPHER * imports
- DelayedArray * imports
- DelayedMatrixStats * imports
- DirichletMultinomial * imports
- IRanges * imports
- MASS * imports
- S4Vectors * imports
- ape * imports
- decontam * imports
- dplyr * imports
- methods * imports
- rlang * imports
- scater * imports
- scuttle * imports
- stats * imports
- tibble * imports
- tidyr * imports
- utils * imports
- vegan * imports
- BiocStyle * suggests
- ade4 * suggests
- biomformat * suggests
- dada2 * suggests
- knitr * suggests
- microbiomeDataSets * suggests
- patchwork * suggests
- phyloseq * suggests
- reldist * suggests
- rmarkdown * suggests
- stringr * suggests
- testthat * suggests
- yaml * suggests
.github/workflows/check-bioc-devel.yml
actions
- actions/cache v1 composite
- actions/checkout v2 composite
- actions/upload-artifact master composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite