phylosmith
phylosmith: an R-package for reproducible and efficient microbiome analysis with phyloseq-objects - Published in JOSS (2019)
Science Score: 95.0%
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 and JOSS metadata -
✓Academic publication links
Links to: plos.org, joss.theoj.org, zenodo.org -
✓Committers with academic emails
2 of 4 committers (50.0%) from academic institutions -
○Institutional organization owner
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✓JOSS paper metadata
Published in Journal of Open Source Software
Scientific Fields
Repository
functions for analyzing phyloseq data
Basic Info
- Host: GitHub
- Owner: schuyler-smith
- License: gpl-3.0
- Language: R
- Default Branch: master
- Homepage: https://schuyler-smith.github.io/phylosmith/
- Size: 56 MB
Statistics
- Stars: 28
- Watchers: 1
- Forks: 3
- Open Issues: 1
- Releases: 1
Metadata Files
README.md
phylosmith
A supplementary package to build on the phyloseq package. Phyloseq objects are a great data-standard for microbiome and gene-expression data, this package is aimed to provied easy data-wrangling and visualization.
Installation
Requirements
Linux Systems
For some Linux systems you may need to install the following two programs through your terminal.
Ubuntu example:
bash
sudo apt-get install libmysqlclient-dev libgdal-dev libudunits2-dev libfontconfig1-dev
These programs are required by some dependencies and may not come in your default OS distribution.
Windows Systems
if you are working on WINDOWS you likely need to install the CRAN program Rtools. When prompted, select add rtools to system PATH.
R
phylosmith depends on the usage of the phyloseq package released by Dr. Paul McMurdie. The package is maintained on BioConductor, and can be installed through R using the following commands:
if(!requireNamespace("BiocManager", quietly = TRUE)){
install.packages("BiocManager")
}
BiocManager::install("phyloseq")
Additionally, the package imports a number of other packages to use their advanced functions. These packages may install with the phylosmith installation, but it is always best to install independently.
install.packages(c("devtools", "RcppEigen", "RcppParallel", "Rtsne", "ggforce", "units"))
phylosmith
The package is hosted on Github, and can be installed through R with:
remotes::install_github('schuyler-smith/phylosmith')
library(phylosmith)
Owner
- Name: Schuyler Smith
- Login: schuyler-smith
- Kind: user
- Location: Champaign, IL
- Website: https://schuyler-smith.github.io/
- Repositories: 3
- Profile: https://github.com/schuyler-smith
Bioinformatics and Computational Science
JOSS Publication
phylosmith: an R-package for reproducible and efficient microbiome analysis with phyloseq-objects
Authors
Department of Bioinformatics and Computational Biology, Iowa State University
Editor
Karthik Ram
Tags
microbiology microbiome metagenomics microbial ecologyGitHub Events
Total
- Issues event: 3
- Watch event: 1
- Issue comment event: 9
- Push event: 6
- Pull request event: 6
Last Year
- Issues event: 3
- Watch event: 1
- Issue comment event: 9
- Push event: 6
- Pull request event: 6
Committers
Last synced: 5 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Schuyler Smith | s****h@i****u | 461 |
| schuyler-smith | s****h@n****m | 23 |
| Daniel S. Katz | d****z@i****g | 1 |
| schuyler-smith | s****h@n****m@S****l | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 4 months ago
All Time
- Total issues: 30
- Total pull requests: 8
- Average time to close issues: 3 months
- Average time to close pull requests: 1 minute
- Total issue authors: 25
- Total pull request authors: 2
- Average comments per issue: 2.97
- Average comments per pull request: 0.0
- Merged pull requests: 8
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 3
- Pull requests: 6
- Average time to close issues: 2 months
- Average time to close pull requests: less than a minute
- Issue authors: 3
- Pull request authors: 1
- Average comments per issue: 1.67
- Average comments per pull request: 0.0
- Merged pull requests: 6
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- Madegwa (2)
- vee3capp (2)
- joey711 (2)
- rogarcia1992 (2)
- dikiprawisuda (2)
- jcmcnch (1)
- mortuseon (1)
- benedil (1)
- karthik (1)
- ctekellogg (1)
- ignadb (1)
- OriolGEM (1)
- lucaswauters (1)
- JacobRPrice (1)
- elayton13 (1)
Pull Request Authors
- schuyler-smith (8)
- danielskatz (1)
Top Labels
Issue Labels
Pull Request Labels
Dependencies
- R >= 3.5 depends
- RColorBrewer * imports
- RcppParallel * imports
- Rtsne * imports
- data.table * imports
- ggplot2 * imports
- ggraph * imports
- ggrepel * imports
- grDevices * imports
- igraph * imports
- parallel * imports
- phyloseq * imports
- sf * imports
- stats * imports
- stringr * imports
- vegan * imports
- BiocStyle * suggests
- devtools * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests