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https://github.com/animesh/microbiomemarker

R package for microbiome biomarker discovery

https://github.com/animesh/microbiomemarker

Science Score: 23.0%

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

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    Found 63 DOI reference(s) in README
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    Links to: zenodo.org
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    Low similarity (15.5%) to scientific vocabulary
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R package for microbiome biomarker discovery

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Fork of yiluheihei/microbiomeMarker
Created almost 4 years ago · Last pushed about 4 years ago

https://github.com/animesh/microbiomeMarker/blob/master/ 



# microbiomeMarker





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***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
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
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): 118.
    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): 12001202. 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): 111. 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): 117. 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): 13940. 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): 121. 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.
    
-   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.
    
-   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.
    
-   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.
    
-   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.
    
-   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.
    
-   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. 
-   Molinero N, Taladrid D, Zorraqun-Pea I, et al.Ulcerative Colitis
    Seems to Imply Oral Microbiome Dysbiosis. Current Issues in
    Molecular Biology, 2022, 44(4): 1513-1527.
    
-   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. 
-   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.
    
-   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.
    
-   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. 
-   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. 
-   Shanmugam G, Lee SH, Jeon J. EzMAP: Easy Microbiome Analysis
    Platform. BMC bioinformatics. 2021 Dec;22(1):1-0.
    
-   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.
    
-   Knstner 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.
    
-   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. 
-   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.
    

## 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

and .

    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: Ani
  • Login: animesh
  • Kind: user
  • Location: Norway
  • Company: Norwegian University of Science and Technology

A medical graduate from Delhi University with post-graduation in bioinformatics from Jawaharlal Nehru University, India.

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