| WGS Sequence data |
NCBI SRA |
https://www.ncbi.nlm.nih.gov/sra |
| Bioinformatics Analysis Code |
Github |
https://github.com/huananfshi/microbiome_multiomics_analysis_workflow |
| KneadData (version 0.73) |
|
https://huttenhower.sph.harvard.edu/kneaddata |
| MetaPhlAn (version 3.0.2) |
[Reference 32] |
https://huttenhower.sph.harvard.edu/metaphlan |
| HUMAnN (version 3.0.0.alpha.3) |
[Reference 33] |
https://huttenhower.sph.harvard.edu/humann |
| LEfSe |
[Reference 41] |
https://huttenhower.sph.harvard.edu/lefse |
| R (version 3.6.3) |
|
http://r-project.org/ |
| R Studio (version 1.2.5033) |
|
https://rstudio.com/ |
| DADA2 (version 1.14.1) |
Bioconductor |
https://www.bioconductor.org/packages/release/bioc/html/dada2.html |
| WRS2 (version 1.1.0) |
[Reference 25] |
https://cran.r-project.org/web/packages/WRS2/ |
| Vegan (version 2.5.7) |
[Reference 40] |
https://cran.r-project.org/web/packages/vegan/index.html |
| mixOmics (version 6.10.9) |
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/mixOmics.html |
| RVAideMemoire (version 0.9.78) |
|
https://cran.r-project.org/web/packages/RVAideMemoire/index.html |
| ComplexHeatmap (version 2.2.0) |
Bioconductor |
https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html |
| Scikit-learn (version 0.21.3) |
[Reference 36] |
https://scikit-learn.org/ |
| Scipy (version 1.5.1) |
|
https://www.scipy.org/ |
| Statsmodels (version 0.9.0) |
|
https://www.statsmodels.org/ |
| Pandas (version 0.24.2) |
|
https://pandas.pydata.org/ |
| Python (version 3.7.6) |
|
https://www.python.org/ |
| Seaborn (version 0.10.1) |
|
https://seaborn.pydata.org/ |
| Jupyter Notebook (version 6.1.4) |
|
https://jupyter.org/ |
