Science Score: 49.0%
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
Found .zenodo.json file -
✓DOI references
Found 2 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
5 of 11 committers (45.5%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.0%) to scientific vocabulary
Keywords from Contributors
Repository
R shiny app for interactive microbiome analysis
Basic Info
- Host: GitHub
- Owner: wejlab
- License: other
- Language: R
- Default Branch: devel
- Homepage: https://wejlab.github.io/animalcules-docs/
- Size: 18.6 MB
Statistics
- Stars: 55
- Watchers: 6
- Forks: 22
- Open Issues: 1
- Releases: 0
Metadata Files
README.md
animalcules 
What does animalcules do?
R shiny app for interactive microbiome analysis
animalcules is an R package for utilizing up-to-date data analytics, visualization methods, and machine learning models to provide users an easy-to-use interactive microbiome analysis framework. It can be used as a standalone software package or users can explore their data with the accompanying interactive R Shiny application.
Traditional microbiome analysis such as alpha/beta diversity and differential abundance analysis are enhanced, while new methods like biomarker identification are introduced by animalcules. Powerful interactive and dynamic figures generated by animalcules enable users to understand their data better and discover new insights.
Documentation
Please check our website at https://wejlab.github.io/animalcules-docs/
Citation
Our paper on animalcules was published on the journal Microbiome in 2021!
You can find our paper here: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01013-0
Please cite:
Zhao, Y., Federico, A., Faits, T., Manimaran, S., Segrè, D., Monti, S. and Johnson, W.E., 2021. animalcules: interactive microbiome analytics and visualization in R. Microbiome, 9(1), pp.1-16.
Before Installation
- Make sure R version is >= 4.3.0 and Bioconductor version is 3.18. Bioconductor could be updated by :
r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(version = "3.18")
Installation
- Install the release version of the package from Bioconductor
``` r if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("wejlab/animalcules")
```
- Install the development version of the package from Github
r
if (!requireNamespace("devtools", quietly=TRUE))
install.packages("devtools")
devtools::install_github("wejlab/animalcules")
Run the animalcules shiny app!
r
library(animalcules)
run_animalcules()
Installing w/ Docker
First, make sure you have Docker installed on your machine.
- Pull the pre-built Docker image
docker pull bucbm/animalcules:latest
- Or if you'd like to build the Docker image from scratch
bash
git clone https://github.com/wejlab/animalcules
cd animalcules
docker build --tag bucbm/animalcules:latest .
Run with Docker
bash docker run -d -p 8787:8787 -e PASSWORD=animalcules bucbm/animalcules:latestGo to http://localhost:8787/ in browser and enter username: rstudio / password: animalcules. Then enter the following:
r
library(animalcules)
run_animalcules()
Owner
- Name: W. Evan Johnson Lab
- Login: wejlab
- Kind: organization
- Email: wejlab@gmail.com
- Location: United States of America
- Website: www.wejlab.org
- Twitter: wejlab
- Repositories: 1
- Profile: https://github.com/wejlab
This is the main GitHub home for the research and software projects from Evan Johnson's Lab
GitHub Events
Total
- Issues event: 1
- Watch event: 3
- Issue comment event: 1
- Push event: 2
- Pull request event: 1
- Fork event: 4
Last Year
- Issues event: 1
- Watch event: 3
- Issue comment event: 1
- Push event: 2
- Pull request event: 1
- Fork event: 4
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| jasonzhao0307 | j****7@g****m | 212 |
| Anthony Federico | a****o@u****m | 110 |
| jessmcc22Mac | j****c@b****u | 41 |
| Nitesh Turaga | n****a@g****m | 14 |
| W. Evan Johnson | w****j@b****u | 13 |
| J Wokaty | j****y@s****u | 6 |
| J Wokaty | j****y@u****m | 4 |
| A Wokaty | a****y@s****u | 2 |
| Aubrey Odom | a****m@b****u | 2 |
| Hervé Pagès | h****b@g****m | 1 |
| Hervé Pagès | h****s@f****g | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 7 months ago
All Time
- Total issues: 47
- Total pull requests: 24
- Average time to close issues: 3 months
- Average time to close pull requests: 5 days
- Total issue authors: 11
- Total pull request authors: 3
- Average comments per issue: 0.87
- Average comments per pull request: 0.04
- Merged pull requests: 21
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 1
- Pull requests: 1
- Average time to close issues: 11 months
- Average time to close pull requests: less than a minute
- Issue authors: 1
- Pull request authors: 1
- Average comments per issue: 2.0
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- jasonzhao0307 (31)
- anfederico (3)
- Zinthrow (3)
- IdanBanson (3)
- davitero (1)
- s6aamani (1)
- aubreyodom (1)
- nunrath (1)
- cjfields (1)
- jarrodscott (1)
- ReneKat (1)
Pull Request Authors
- jessmcc22 (27)
- wevanjohnson (4)
- sktpndt97 (3)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
-
Total downloads:
- bioconductor 17,862 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 7
- Total maintainers: 1
bioconductor.org: animalcules
Interactive microbiome analysis toolkit
- Homepage: https://github.com/wejlab/animalcules
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/animalcules/inst/doc/animalcules.pdf
- License: Artistic-2.0
-
Latest release: 1.24.0
published 12 months ago
Rankings
Maintainers (1)
Dependencies
- R >= 4.0.0 depends
- DESeq2 * imports
- DT * imports
- GUniFrac * imports
- Matrix * imports
- MultiAssayExperiment * imports
- S4Vectors >= 0.23.19 imports
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