genomeSeq

Research project in metagenomics and microbiome.

This repository is destined to keep register of the data analysis and to share scripts and code.

Description of files in this repository

• spermosphere-logbook.ipynb keeps a record of the data analysis of spermospheric soil samples coming from different accessions of Phaseolus vulgaris.
• rizhosphere-logbook.ipynb keeps a record of the data analysis of rhizospheric soil samples coming from different accessions of Phaseolus vulgaris.
• proyect-files.txt shows a list of project files in tree format.
• The directory metagenomeSeq-abund contains data concerning differential abundance analysis carried out with metagenomeSeq package in R.
• The directory spermosphere contains the files metadata.tsv, table.qza and rep-seqs.qza from the spermosphere data.
• The directory rhizosphere contains the files metadata.tsv, table.qza and rep-seqs.qza from the rhizosphere data.

Useful information and resources

Using Git and GitHub in science

• Git for Scientists by Miles McBain.

Very nice review about microbiome analysis

• Knight, R., Vrbanac, A., Taylor, B.C. et al. Best practices for analysing microbiomes. Nat Rev Microbiol 16, 410–422 (2018). https://doi.org/10.1038/s41579-018-0029-9

On the importance of keeping a laboratory notebook (even if working in bioinformatics)

• Schnell S (2015) Ten Simple Rules for a Computational Biologist’s Laboratory Notebook. PLoS Comput Biol 11(9): e1004385. https://doi.org/10.1371/journal.pcbi.1004385
• How to Keep a Lab Notebook for Bioinformatic Analyses
• How to keep a lab notebook

Universidad de Antioquia, Colombia.