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rbiom

An R Package for Streamlined Microbiome Analysis and Automated Statistical Visualization

https://github.com/cmmr/rbiom

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 1 committers (100.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (19.6%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

An R Package for Streamlined Microbiome Analysis and Automated Statistical Visualization

Basic Info
Statistics
  • Stars: 18
  • Watchers: 6
  • Forks: 1
  • Open Issues: 3
  • Releases: 6
Created about 9 years ago · Last pushed 11 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = '#>',
  fig.path = 'man/figures/README-',
  fig.height = 4,
  fig.width = 8,
  dev='ragg_png'
)
```

# rbiom rbiom logo


[![cran](https://www.r-pkg.org/badges/version/rbiom)](https://CRAN.R-project.org/package=rbiom)
[![conda](https://anaconda.org/conda-forge/r-rbiom/badges/version.svg)](https://anaconda.org/conda-forge/r-rbiom)
[![downloads](https://cranlogs.r-pkg.org/badges/grand-total/rbiom)](https://cranlogs.r-pkg.org/)
[![covr](https://codecov.io/gh/cmmr/rbiom/graph/badge.svg)](https://app.codecov.io/gh/cmmr/rbiom)



`rbiom` is designed for microbiome researchers, providing visualizations and 
statistical analyses from Biological Observation Matrix (BIOM) files.


## Installation

The latest stable version can be installed from CRAN.

``` r
install.packages('rbiom')
```

The development version is available on GitHub.

``` r
install.packages('pak')
pak::pak('cmmr/rbiom')
```


## Usage

#### Import and rarefy abundance counts.
```{r usage}
library(rbiom)

infile <- system.file(package = 'rbiom', 'extdata', 'hmp50.bz2')
biom   <- rarefy(infile)
```


#### Explore associations with metadata.
```{r bdiv}
bdiv_ord_plot(biom, stat.by = 'Body Site', facet.by = 'Sex')
adiv_boxplot(biom, x = 'Sex', adiv = c('otu', 'shan'), stat.by = 'Body Site')
subset(biom, `Body Site` == 'Buccal mucosa') %>% 
  taxa_corrplot('Age', taxa = 2, layers = 'ptc', fit = 'lm', test = 'emtrends')
```


#### Summarize counts by taxonomic rank.
```{r taxa}
taxa_heatmap(biom, taxa = 10, tracks = c('body', 'age'))
taxa_stacked(biom, rank = 'Phylum')
taxa_table(biom, 'Phylum')
```



## Documentation

The online manual for `rbiom` is available at https://cmmr.github.io/rbiom/. It includes a getting started guide, articles that explore specific use cases, and reference pages for each function.


## Community guidelines

### Support

Bug reports, feature requests, and general questions can be submitted at https://github.com/cmmr/rbiom/issues.

### Contributing

Pull requests are welcome. Please ensure contributed code is covered by tests and documentation (add additional tests and documentation as needed) and that it passes all automated tests.



## Automated tests

The following commands will check if `rbiom` passes the bundled testing suite.

```r
install.packages('testthat')
testthat::test_check('rbiom')
```

Owner

  • Name: Alkek Center for Metagenomics and Microbiome Research
  • Login: cmmr
  • Kind: organization
  • Location: Baylor College of Medicine, Houston TX

CMMR researchers develop molecular and informatic tools to advance clinical microbiome research.

GitHub Events

Total
  • Create event: 5
  • Release event: 4
  • Issues event: 14
  • Watch event: 6
  • Issue comment event: 15
  • Push event: 146
  • Pull request review event: 3
  • Pull request review comment event: 2
  • Pull request event: 2
Last Year
  • Create event: 5
  • Release event: 4
  • Issues event: 14
  • Watch event: 6
  • Issue comment event: 15
  • Push event: 146
  • Pull request review event: 3
  • Pull request review comment event: 2
  • Pull request event: 2

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 238
  • Total Committers: 1
  • Avg Commits per committer: 238.0
  • Development Distribution Score (DDS): 0.0
Past Year
  • Commits: 25
  • Committers: 1
  • Avg Commits per committer: 25.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Daniel Smith d****h@o****u 238
Committer Domains (Top 20 + Academic)
orst.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 28
  • Total pull requests: 1
  • Average time to close issues: about 2 months
  • Average time to close pull requests: about 10 hours
  • Total issue authors: 12
  • Total pull request authors: 1
  • Average comments per issue: 2.43
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 9
  • Pull requests: 1
  • Average time to close issues: 16 days
  • Average time to close pull requests: about 10 hours
  • Issue authors: 4
  • Pull request authors: 1
  • Average comments per issue: 1.89
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • dansmith01 (9)
  • shwetha141 (5)
  • nick-youngblut (2)
  • chrysn (2)
  • ibrila (1)
  • hberger (1)
  • jayelldubya (1)
  • colin-heberling (1)
  • akbrand6 (1)
  • SilasK (1)
  • marianovosolov (1)
  • TKMarkCheng (1)
Pull Request Authors
  • teunbrand (1)
  • TKMarkCheng (1)
Top Labels
Issue Labels
enhancement (2) bug (1)
Pull Request Labels

Packages

  • Total packages: 2
  • Total downloads:
    • cran 23,556 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 2
    (may contain duplicates)
  • Total versions: 12
  • Total maintainers: 1
cran.r-project.org: rbiom

Read/Write, Analyze, and Visualize 'BIOM' Data

  • Versions: 10
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 23,556 Last month
Rankings
Dependent repos count: 19.2%
Stargazers count: 20.6%
Average: 27.4%
Forks count: 27.8%
Dependent packages count: 28.7%
Downloads: 40.9%
Maintainers (1)
dansmith01@gmail.com
Last synced: 11 months ago
conda-forge.org: r-rbiom
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent repos count: 34.0%
Average: 49.9%
Dependent packages count: 51.2%
Stargazers count: 53.5%
Forks count: 61.1%
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.5.0 depends
  • R.utils * imports
  • Rcpp * imports
  • RcppParallel * imports
  • ape * imports
  • broom * imports
  • ggbeeswarm * imports
  • ggnewscale * imports
  • ggpattern * imports
  • ggplot2 * imports
  • ggrepel * imports
  • ggtext * imports
  • glue * imports
  • gridpattern * imports
  • jsonlite * imports
  • magick * imports
  • magrittr * imports
  • memoise * imports
  • methods * imports
  • openxlsx * imports
  • paletteer * imports
  • patchwork * imports
  • pheatmap * imports
  • plyr * imports
  • rlang * imports
  • slam * imports
  • tidyr * imports
  • tsne * imports
  • uwot * imports
  • vegan * imports
  • ggdensity * suggests
  • reshape2 * suggests
  • rhdf5 * suggests
  • testthat * suggests