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microbiomeMarker

R package for microbiome biomarker discovery

https://github.com/yiluheihei/microbiomemarker

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
  • ✓
    DOI references
    Found 63 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ○
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  • ○
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  • ○
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    Low similarity (15.9%) to scientific vocabulary

Keywords

biomarker-discovery differential-abundance-analysis lefse metagenomics microbiome r r-package
Last synced: 6 months ago · JSON representation

Repository

R package for microbiome biomarker discovery

Basic Info
Statistics
  • Stars: 189
  • Watchers: 10
  • Forks: 41
  • Open Issues: 56
  • Releases: 1
Topics
biomarker-discovery differential-abundance-analysis lefse metagenomics microbiome r r-package
Created over 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License

README.Rmd 

---
title:: R package for microbiome biomarker discovery
output: github_document
---



# microbiomeMarker




[![](https://img.shields.io/badge/release%20version-1.2.1-green.svg)](https://www.bioconductor.org/packages/microbiomeMarker)
[![](https://img.shields.io/badge/devel%20version-1.3.2-green.svg)](https://github.com/yiluheihei/microbiomeMarker)
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![GitHub Repo stars](https://img.shields.io/github/stars/yiluheihei/microbiomeMarker?style=social)


***microbiomeMarker*** is still under development, your suggestion and contribution will be highly appreciated. If you think this project is helpful to you, you can give this project a :star:.

## Motivation

The aim of this package is to build a unified toolbox in R for microbiome 
biomarker discovery by integrating existing widely used differential analysis methods.

## Installation

Install the package from Bioconductor directly:

```{r install-bioc,eval=FALSE}
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("microbiomeMarker")
```

Or install the development version of the package from
[Github](https://github.com/yiluheihei/microbiomeMarker). 

```{r install-gh,eval=FALSE}
if (!requireNamespace("remotes", quietly=TRUE))
  install.packages("remotes")
remotes::install_github("yiluheihei/microbiomeMarker")
```

For more details on how to use ***microbiomeMarker***, please see the help page 
or [website](https://yiluheihei.github.io/microbiomeMarker/index.html) of our 
package.

## Citation

Kindly cite as follows: 

**Yang Cao**, Qingyang Dong, Dan Wang, Pengcheng Zhang, Ying Liu, Chao 
Niu, microbiomeMarker: an R/Bioconductor package for microbiome marker 
identification and visualization. Bioinformatics, 2022, btac438. doi: [10.1093/bioinformatics/btac438](https://doi.org/10.1093/bioinformatics/btac438)

Please cite the corresponding methods paper too:

- LEfSe: Segata, Nicola, Jacques Izard, et al. 2011. Metagenomic Biomarker 
  Discovery and Explanation. Genome Biology 12 (6): 1–18. 
  doi: [10.1186/gb-2011-12-6-r60](https://doi.org/10.1186/gb-2011-12-6-r60)
- metagenomeSeq: Paulson, Joseph N, O Colin Stine, et al. 2013. Differential 
  Abundance Analysis for Microbial Marker-Gene Surveys. Nature Methods 10 (12): 
  1200–1202. doi: [10.1038/nmeth.2658](https://doi.org/10.1038/nmeth.2658)
- ANCOM: Mandal, Siddhartha, Will Van Treuren, et al. 2015. Analysis of 
  Composition of Microbiomes: A Novel Method for Studying Microbial Composition.
  Microbial Ecology in Health and Disease 26 (1): 27663. 
  doi: [10.3402/mehd.v26.27663](https://doi.org/10.3402/mehd.v26.27663)
- ANCOMBC: Lin, Huang, and Shyamal Das Peddada. 2020. Analysis of Compositions 
  of Microbiomes with Bias Correction. Nature Communications 11 (1): 1–11. 
   doi: [10.1038/s41522-020-00160-w](https://doi.org/10.1038/s41522-020-00160-w)
- ALDEx2: Fernandes, Andrew D, Jennifer Ns Reid, et al. 2014. Unifying the 
  Analysis of High-Throughput Sequencing Datasets: Characterizing Rna-Seq, 16S 
  rRNA Gene Sequencing   and Selective Growth Experiments by Compositional Data 
  Analysis.  Genome Biology 15(2): 1–17. 
  doi: [10.1186/2049-2618-2-15](https://doi.org/10.1186/2049-2618-2-15)
- edgeR: Robinson, Mark D, Davis J McCarthy, and Gordon K Smyth. 2010. EdgeR: A
  Bioconductor Package for Differential Expression Analysis of Digital Gene 
  Expression Data. Bioinformatics 26 (1): 139–40. doi: 
  [10.1093/bioinformatics/btp616](https://doi.org/10.1093/bioinformatics/btp616)
- DESeq2: Love, Michael I, Wolfgang Huber, and Simon Anders. 2014. Moderated 
  Estimation of Fold Change and Dispersion for Rna-Seq Data with Deseq2. Genome 
  Biology 15 (12): 1–21. 
  doi: [10.1186/s13059-014-0550-8](https://doi.org/10.1186/s13059-014-0550-8)
- limma-voom: Law, Charity W, Yunshun Chen, et al. 2014. Voom: Precision Weights
  Unlock Linear Model Analysis Tools for Rna-Seq Read Counts. Genome biology, 
  15(2), 1-17. 
  doi: [10.1186/gb-2014-15-2-r29](https://doi.org/10.1186/gb-2014-15-2-r29)

### Publications citing microbiomeMarker

- Jorge F, Froissard C, Dheilly N M, et al. Bacterial community dynamics
  following antibiotic exposure in a trematode parasite. International 
  journal for parasitology, 2022, 52(5): 265-274. 
  https://doi.org/10.1016/j.ijpara.2021.11.006
- Ghosh A, Thakur M, Sharma L K, et al. Linking gut microbiome with the feeding
  behavior of the Arunachal macaque (Macaca munzala). Scientific reports, 2021,
  11(1): 1-10. https://doi.org/10.1038/s41598-021-01316-0
- Doi R, Wu Y, Kawai Y, et al. Transition and regulation mechanism of bacteria 
  biota   in Kishu saba-narezushi (mackerel narezushi) during its fermentation 
  step. Journal of bioscience and bioengineering, 2021, 132(6): 606-612. 
  https://doi.org/10.1016/j.jbiosc.2021.09.002
- Nielsen K R, Ingham A C, Midjord J, et al. Similar Gut Bacterial Composition
  Between Patients With Ulcerative Colitis and Healthy Controls in a High
  Incidence Population: A Cross-sectional Study of the Faroe Islands IBD Cohort.
  Inflammatory Bowel Diseases. https://doi.org/10.1093/ibd/izab355
- Prevel R, Enaud R, Orieux A, et al. Gut bacteriobiota and mycobiota are both
  associated with Day-28 mortality among critically ill patients. Critical Care,
  2022, 26(1): 1-9. https://doi.org/10.1186/s13054-022-03980-8
- Tandon K, Chiou Y J, Yu S P, et al. Microbiome restructuring: dominant coral
  bacterium Endozoicomonas species display differential adaptive capabilities 
  to environmental changes[J]. bioRxiv, 2021.
  https://doi.org/10.1101/2021.10.31.466697
- Dai D, Zhu J, Sun C, et al. GMrepo v2: a curated human gut microbiome database
  with special focus on disease markers and cross-dataset comparison. Nucleic 
  acids research, 2022, 50(D1): D777-D784. https://doi.org/10.1093/nar/gkab1019
- Molinero N, Taladrid D, Zorraquín-Peña I, et al. Ulcerative Colitis Seems to 
  Imply Oral Microbiome Dysbiosis. Current Issues in Molecular Biology, 2022,
  44(4): 1513-1527. https://doi.org/10.3390/cimb44040103
- Ricci F, Tandon K, Black J R, et al. Host Traits and Phylogeny Contribute to
  Shaping Coral-Bacterial Symbioses[J]. Msystems, 2022, 7(2): e00044-22.
  https://doi.org/10.1128/msystems.00044-22
- Chavarria K A, Saltonstall K, Vinda J, et al. Land use influences stream 
  bacterial communities in lowland tropical watersheds. Scientific reports, 
  2021, 11(1): 1-12. https://doi.org/10.1038/s41598-021-01193-7
- Lu H, Gao N L, Tong F, et al. Alterations of the Human Lung and Gut 
  Microbiomes in Non-Small Cell Lung Carcinomas and Distant Metastasis. 
  Microbiology spectrum, 2021, 9(3): e00802-21.
  https://doi.org/10.1128/Spectrum.00802-21
- Ingham A C, Kielsen K, Mordhorst H, et al. Microbiota long-term dynamics and
  prediction of acute graft-versus-host disease in pediatric allogeneic stem 
  cell transplantation[J]. Microbiome, 2021, 9(1): 1-28.
  https://doi.org/10.1186/s40168-021-01100-2
- Wang R, Cao S, Bashir M E H, et al. Microbial metabolite butyrate-prodrug
  polymeric micelles promote gut health and treat food allergies. bioRxiv, 
  2022. https://doi.org/10.1101/2022.05.01.490224
- Shanmugam G, Lee SH, Jeon J. EzMAP: Easy Microbiome Analysis Platform. BMC
  bioinformatics. 2021 Dec;22(1):1-0. 
  https://doi.org/10.1186/s12859-021-04106-7
- Altaib H, Nakamura K, Abe M, et al. Differences in the concentration of the 
  fecal neurotransmitters GABA and glutamate are associated with microbial 
  composition among healthy human subjects. Microorganisms. 2021. Feb;9(2):378. 
  https://doi.org/10.3390/microorganisms9020378
- Künstner A, Aherrahrou R, Hirose M, et al. Effect of Differences in the 
  Microbiome of Cyp17a1-Deficient Mice on Atherosclerotic Background. Cells. 
  2021 Jun;10(6):1292. https://doi.org/10.3390/cells10061292
- Ingham AC, Urth TR, Sieber RN, et al. Dynamics of the human nasal microbiota 
  and Staphylococcus aureus CC398 carriage in pig truck drivers across one 
  workweek. Applied and Environmental Microbiology. 2021 Jun 30:AEM-01225.
  https://doi.org/10.1128/AEM.01225-21
- Shibata T, Nakagawa M, Coleman HN, et al. Evaluation of DNA extraction 
  protocols from liquid-based cytology specimens for studying cervical 
  microbiota. Plos one 16, no. 8 2021. https://doi.org/10.1371/journal.pone.0237556

## Question

If you have any question, please file an issue on the issue tracker following 
the instructions in the issue template:

Please briefly describe your problem, what output actually happened, and what 
output you expect.

Please provide a minimal reproducible example. For more details on how to make 
a great minimal reproducible example, see https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example 
and https://www.tidyverse.org/help/#reprex.

```
Brief description of the problem

# insert minimal reprducible example here
```

## Acknowledgement

We thanks all the developers of the methods integrated into our package.

- [lefse python script](https://bitbucket.org/biobakery/biobakery/wiki/lefse), 
  The main lefse code are translated from ***lefse python script***,
- [microbiomeViz](https://github.com/lch14forever/microbiomeViz), cladogram 
  visualization of lefse is modified from ***microbiomeViz***.
- [phyloseq](https://github.com/joey711/phyloseq), the main data structures used 
  in ***microbiomeMarker*** are from or inherit from `phyloseq-class` in package 
  ***phyloseq***.
- [MicrobiotaProcess](https://github.com/YuLab-SMU/MicrobiotaProcess), function 
  `import_dada2()` and `import_qiime2()` are modified from the 
  `MicrobiotaProcess::import_dada2()`.
- [qiime2R](https://github.com/jbisanz/qiime2R), `import_qiime2()` are refer to 
  the functions in ***qiime2R***.

Owner

  • Name: Yang Cao
  • Login: yiluheihei
  • Kind: user
  • Location: Tianjin

R, Bioinformatics

GitHub Events

Total
  • Issues event: 4
  • Watch event: 16
  • Issue comment event: 8
  • Push event: 6
  • Fork event: 1
  • Create event: 1
Last Year
  • Issues event: 4
  • Watch event: 16
  • Issue comment event: 8
  • Push event: 6
  • Fork event: 1
  • Create event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 255
  • Total Committers: 3
  • Avg Commits per committer: 85.0
  • Development Distribution Score (DDS): 0.024
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
yiluheihei y****i@g****m 249
Nitesh Turaga n****a@g****m 4
bioBDAI-hui123 h****1@g****m 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 97
  • Total pull requests: 1
  • Average time to close issues: 2 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 74
  • Total pull request authors: 1
  • Average comments per issue: 2.09
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 6
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 6
  • Pull request authors: 0
  • Average comments per issue: 1.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • marwa38 (8)
  • akhst7 (5)
  • mawa86 (3)
  • fconstancias (3)
  • Roedani (2)
  • LDoni (2)
  • acmasche (2)
  • cpavloud (2)
  • SonWende (2)
  • LeeJH5120 (2)
  • mdtorohernando (2)
  • DrYoungOG (2)
  • vjcitn (1)
  • bahyirou (1)
  • phuongdoand (1)
Pull Request Authors
  • yanhui09 (1)
Top Labels
Issue Labels
feature (1) lefse (1) bug (1)
Pull Request Labels

Packages

  • Total packages: 3
  • Total downloads:
    • bioconductor 20,233 total
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 0
    (may contain duplicates)
  • Total versions: 9
  • Total maintainers: 1
proxy.golang.org: github.com/yiluheihei/microbiomemarker
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
proxy.golang.org: github.com/yiluheihei/microbiomeMarker
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 6 months ago
bioconductor.org: microbiomeMarker

microbiome biomarker analysis toolkit

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 20,233 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Stargazers count: 1.0%
Forks count: 1.1%
Average: 12.3%
Downloads: 59.2%
Maintainers (1)
caoyang.name@gmail.com
Last synced: 6 months ago

Dependencies

.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc master composite
  • r-lib/actions/setup-r master composite
.github/workflows/pkgdown.yaml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • r-lib/actions/setup-pandoc v1 composite
  • r-lib/actions/setup-r v1 composite
DESCRIPTION cran
  • R >= 4.1.0 depends
  • ALDEx2 * imports
  • ANCOMBC * imports
  • Biobase * imports
  • BiocGenerics * imports
  • BiocParallel * imports
  • Biostrings * imports
  • ComplexHeatmap * imports
  • DESeq2 * imports
  • IRanges * imports
  • MASS * imports
  • S4Vectors * imports
  • biomformat * imports
  • caret * imports
  • coin * imports
  • dplyr * imports
  • edgeR * imports
  • ggplot2 * imports
  • ggsignif * imports
  • ggtree * imports
  • limma * imports
  • magrittr * imports
  • metagenomeSeq * imports
  • methods * imports
  • multtest * imports
  • pROC * imports
  • patchwork * imports
  • phyloseq * imports
  • plotROC * imports
  • purrr * imports
  • rlang * imports
  • stats * imports
  • tibble * imports
  • tidyr * imports
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  • yaml * imports
  • BiocStyle * suggests
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  • glmnet * suggests
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  • knitr * suggests
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