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# 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): 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***.