MicrobiotaProcess

:microbe: A comprehensive R package for deep mining microbiome

https://github.com/yulab-smu/microbiotaprocess

Science Score: 59.0%

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
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 1 DOI reference(s) in README
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Academic publication links
Links to: sciencedirect.com
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Committers with academic emails
1 of 8 committers (12.5%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.3%) to scientific vocabulary

Keywords

microbiome microbiome-analysis microbiome-data rstats

Keywords from Contributors

bioconductor-packages gene bioinformatics ontology single-cell shiny rnaseq genomics core-package u24ca289073

Last synced: 6 months ago · JSON representation

Repository

:microbe: A comprehensive R package for deep mining microbiome

Basic Info

Host: GitHub
Owner: YuLab-SMU
Language: R
Default Branch: master
Homepage: https://www.sciencedirect.com/science/article/pii/S2666675823000164
Size: 6.94 MB

Statistics

Stars: 191
Watchers: 7
Forks: 37
Open Issues: 92
Releases: 0

Topics

microbiome microbiome-analysis microbiome-data rstats

Created almost 7 years ago · Last pushed 8 months ago

Metadata Files

Readme Changelog

README.Rmd

---
output: 
  md_document:
    variant: gfm
html_preview: false
---



# MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

```{r, echo=FALSE, results="hide", message=FALSE}
library(badger)
Biocpkg <- function (pkg) {
    sprintf("[%s](http://bioconductor.org/packages/%s)", pkg, pkg)
}
library(conflicted)
conflicted::conflict_prefer("filter", "dplyr")
knitr::opts_chunk$set(fig.path = "inst/figures/README-")
```

`r badge_bioc_release("MicrobiotaProcess", "green")`
`r badge_devel("YuLab-SMU/MicrobiotaProcess", "green")`
[![Bioc](http://www.bioconductor.org/shields/years-in-bioc/MicrobiotaProcess.svg)](https://www.bioconductor.org/packages/devel/bioc/html/MicrobiotaProcess.html#since)
[![platform](http://www.bioconductor.org/shields/availability/devel/MicrobiotaProcess.svg)](https://www.bioconductor.org/packages/devel/bioc/html/MicrobiotaProcess.html#archives)

+ [**MicrobiotaProcess**](http://bioconductor.org/packages/release/bioc/html/MicrobiotaProcess.html) defines an **MPSE** structure to better integrate both primary and intermediate microbiome datasets.
+ **MicrobiotaProcess** improves the integration and exploration of downstream data analysis.
+ **MicrobiotaProcess** provides a set of functions under a unified tidy framework, which helps users explore related datasets more efficiently.
+ **MicrobiotaProcess** offers many visual methods to quickly render clear and comprehensive visualizations that reveal meaningful insights.

## Anatomy of a **MPSE** 

```{r, echo=FALSE, fig.width = 12, dpi=400, fig.align="center", fig.cap= "The structure of the MPSE class."}
knitr::include_graphics("./inst/figures/mpse.png")
```

## Overview of the design of **MicrobiotaProcess** package

```{r, echo=FALSE, fig.width = 12, dpi=400, fig.align="center", fig.cap="The Overview of the design of MicrobiotaProcess package"}
knitr::include_graphics("./inst/figures/mp-design.png")
```

## :writing_hand: Authors

[Shuangbin Xu](https://github.com/xiangpin) and [Guangchuang Yu](https://guangchuangyu.github.io)

School of Basic Medical Sciences, Southern Medical University

If you use **MicrobiotaProcess** in published research. Please cite the paper:

__Shuangbin Xu__, Li Zhan, Wenli Tang, Qianwen Wang, Zehan Dai, Land Zhou, Tingze Feng, Meijun Chen, Tianzhi Wu, Erqiang Hu, __Guangchuang Yu__^\*. MicrobiotaProcess: A comprehensive R package for deep mining microbiome.__ *The Innovation*__. 2023, 4(2):100388. doi: [10.1016/j.xinn.2023.100388](https://www.sciencedirect.com/science/article/pii/S2666675823000164).

   - [Source code to produce Supplementary Material](https://github.com/YuLab-SMU/MP_supplementary_file)

## :arrow_double_down: Installation

Get the released version from [Bioconductor](https://bioconductor.org/packages/release/bioc/html/MicrobiotaProcess.html):

```r
## try http:// if https:// URLs are not supported ## the url of mirror
if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
## BiocManager::install("BiocUpgrade") ## you may need this
BiocManager::install("MicrobiotaProcess")
```

the development version from github:

```r
if (!requireNamespace("remotes", quietly=TRUE))
    install.packages("remotes")
remotes::install_github("YuLab-SMU/MicrobiotaProcess")
```

# :book: Vignette

For more details, please refer to the [online vignette](https://bioconductor.org/packages/release/bioc/vignettes/MicrobiotaProcess/inst/doc//MicrobiotaProcess.html).

## :sparkling_heart: Contributing

We welcome any contributions! By participating in this project you agree to abide 
by the terms outlined in the [Contributor Code of Conduct](CONDUCT.md).

Owner

Name: Bioinformatics Group @ SMU
Login: YuLab-SMU
Kind: organization
Email: gcyu1@smu.edu.cn
Location: Guangzhou

Website: https://yulab-smu.top
Repositories: 76
Profile: https://github.com/YuLab-SMU

Research group led by Prof. Guangchuang Yu in School of Basic Medical Sciences, Southern Medical University

GitHub Events

Total

Issues event: 10
Watch event: 12
Issue comment event: 2
Push event: 3

Last Year

Issues event: 10
Watch event: 12
Issue comment event: 2
Push event: 3

Committers

Last synced: over 2 years ago

All Time

Total Commits: 1,314
Total Committers: 8
Avg Commits per committer: 164.25
Development Distribution Score (DDS): 0.014

Past Year

Commits: 57
Committers: 3
Avg Commits per committer: 19.0
Development Distribution Score (DDS): 0.07

Top Committers

Name	Email	Commits
xiangpin	x**n@1**m	1,296
Nitesh Turaga	n**a@g**m	10
J Wokaty	j**y@s**u	2
J Wokaty	j****y	2
nyzhoulang	n**g@1**m	1
Lori Shepherd	l**d@r**g	1
Darío Hereñú	m**a@g**m	1
alienzj	a**j@g**m	1

Committer Domains (Top 20 + Academic)

163.com: 2 roswellpark.org: 1 sph.cuny.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 108
Total pull requests: 3
Average time to close issues: about 1 month
Average time to close pull requests: about 2 hours
Total issue authors: 77
Total pull request authors: 3
Average comments per issue: 2.62
Average comments per pull request: 0.33
Merged pull requests: 3
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 10
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 10
Pull request authors: 0
Average comments per issue: 0.0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

liuninghua521 (6)
alienzj (6)
wangkai7 (3)
marwa38 (3)
gregnoel (3)
etorres475 (3)
taekwonleo-yuhao (3)
MonaLiu421 (2)
paiboon-aut (2)
Hua-CM (2)
EsbergA (2)
Junhao-Guo (2)
shaodongyan (2)
1870694249 (2)
akhst7 (2)

Pull Request Authors

nyzhoulang (1)
alienzj (1)
Clearmind777 (1)

Top Labels

Issue Labels

Pull Request Labels

Packages

Total packages: 1
Total downloads:
- bioconductor 32,077 total

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 8
Total maintainers: 1

bioconductor.org: MicrobiotaProcess

A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Homepage: https://github.com/YuLab-SMU/MicrobiotaProcess/
Documentation: https://bioconductor.org/packages/release/bioc/vignettes/MicrobiotaProcess/inst/doc/MicrobiotaProcess.pdf
License: GPL (>= 3.0)
Latest release: 1.20.1
published 9 months ago

Versions: 8
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 32,077 Total

Rankings

Dependent repos count: 0.0%

Dependent packages count: 0.0%

Stargazers count: 1.1%

Forks count: 1.3%

Average: 9.4%

Downloads: 44.7%

Maintainers (1)

xshuangbin@163.com

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 4.0.0 depends
Biostrings * imports
MASS * imports
SummarizedExperiment * imports
ape * imports
coin * imports
dplyr * imports
dtplyr * imports
foreach * imports
ggplot2 * imports
ggrepel * imports
ggsignif * imports
ggstar * imports
ggtree * imports
ggtreeExtra * imports
grDevices * imports
magrittr * imports
methods * imports
patchwork * imports
pillar * imports
plyr * imports
rlang * imports
stats * imports
tibble * imports
tidyr * imports
tidyselect * imports
tidytree >= 0.3.9 imports
treeio >= 1.17.2 imports
utils * imports
vegan * imports
zoo * imports
DECIPHER * suggests
S4Vectors * suggests
aplot * suggests
biomformat * suggests
cli * suggests
corrr * suggests
forcats * suggests
ggVennDiagram * suggests
ggalluvial >= 0.11.1 suggests
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phyloseq * suggests
prettydoc * suggests
purrr * suggests
randomForest * suggests
rmarkdown * suggests
scales * suggests
seqmagick * suggests
testthat * suggests
withr * suggests
yaml * suggests

ecosyste.ms

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Experiments

Open Source Science

MicrobiotaProcess

Science Score: 59.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

GitHub Events

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Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

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Top Labels

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Packages

bioconductor.org: MicrobiotaProcess

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Maintainers (1)

Dependencies