IMAP-PART 08

Exploratory Analysis of 16S-Based Microbial Profiles

Fostering Reproducible Microbiome data Analysis with Snakemake workflow

Deep exploration of microbial profiles

…BRIEF INTRO IN PROGRESS…

Snakemake workflow for exploratory data analysis

A tentative snakemake workflow that defines data exploration rules in a DAG (directed acyclic graph) format. A detailed interactive snakemake HTML report is available here. Use a wider screen to get a better interactive snakemake report.

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Related work

Repo	Description	Status
IMAP-GLIMPSE	IMAP project overview	In-progress
IMAP-PART 01	Software requirement for microbiome data analysis with Snakemake workflows	In-progress
IMAP-PART 02	Downloading and exploring microbiome sample metadata from SRA Database	In-progress
IMAP-PART 03	Downloading and filtering microbiome sequencing data from SRA database	In-progress
IMAP-PART 04	Quality Control of Microbiome Next Generation Sequencing Reads	In-progress
IMAP-PART 05	Microbial profiling using MOTHUR and Snakemake workflows	In-progress
IMAP-PART 06	Microbial profiling using QIIME2 and Snakemake workflows	In-progress
IMAP-PART 07	Processing Output from 16S-Based microbiome bioinformatics pipelines	In-progress
IMAP-PART 08	Exploratory Analysis of 16S-Based Microbiome Processed Data	In-progress
IMAP-PART 09	Exploratory Analysis of 16S-Based Microbiome Processed Data	In-progress
IMAP-PART XX	Predictive Modeling of Microbiome Data Using Machine Learning Techniques	In-progress
IMAP-SUMMARY	Summary of snakemake workflows for microbiome data analysis	In-progress

Citation

Please consider citing the iMAP article^[1] if you find any part of the IMAP practical user guides helpful in your microbiome data analysis.

References

[1]

Buza, T. M., Tonui, T., Stomeo, F., Tiambo, C., Katani, R., Schilling, M., … Kapur, V. (2019). iMAP: An integrated bioinformatics and visualization pipeline for microbiome data analysis. BMC Bioinformatics, 20. https://doi.org/10.1186/S12859-019-2965-4

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Appendix

Project main tree

.
├── LICENSE
├── LICENSE.md
├── README.md
├── Rplots.pdf
├── VennDiagram.2023-04-28_11-18-28.log
├── VennDiagram.2023-04-28_14-24-42.log
├── bs4_viz_books
│   └── markers_analysis.Rmd
├── config
│   └── config.yml
├── dags
│   ├── rulegraph.png
│   └── rulegraph.svg
├── data
│   ├── feature.qza
│   ├── metadata.tsv
│   ├── processed_data.rda
│   ├── shannon.qza
│   └── taxonomy.qza
├── figures
│   ├── ps_caporaso_cladogram-1.png
│   ├── ps_caporaso_heatmap-1.png
│   ├── ps_kostic_crc_cladogram-1.png
│   ├── ps_kostic_crc_heatmap-1.png
│   ├── q2r_barplot.png
│   ├── q2r_barplot.svg
│   ├── q2r_heatmap.png
│   ├── q2r_heatmap.svg
│   ├── q2r_jitterplot.png
│   ├── q2r_jitterplot.svg
│   ├── q2r_pcoa.png
│   ├── q2r_pcoa.svg
│   ├── q2r_venndiagram.png
│   ├── q2r_venndiagram.svg
│   └── unnamed-chunk-7-1.png
├── images
│   ├── coders.png
│   └── explore.png
├── imap-exploratory-analysis.Rproj
├── index.Rmd
├── library
│   ├── apa.csl
│   ├── imap.bib
│   └── references.bib
├── report.html
├── resources
│   ├── feature_table.qza
│   ├── final.biom
│   ├── final.lefse
│   ├── final.shared
│   ├── final.taxonomy
│   ├── metadata.csv
│   ├── rooted_tree.qza
│   ├── sample.final.shared
│   ├── sample_metadata.tsv
│   ├── samples.tsv
│   ├── shannon_vector.qza
│   ├── taxonomy.qza
│   └── unweighted_unifrac_pcoa.qza
├── results
│   └── project_tree.txt
├── styles.css
└── workflow
    ├── Snakefile
    ├── Snakefile_
    ├── envs
    ├── index.Rmd
    ├── report
    ├── rules
    ├── schemas
    ├── scripts
    └── styles.css

15 directories, 57 files

Troubleshooting of FAQs

1. Question
Answer
2. Question
Answer

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Last updated on April 28, 2023.
Github_Repo: https://github.com/tmbuza/imap-exploratory-analysis.
Repo compiled and maintained by: Teresia Mrema-Buza.