phyloassembly
Code for: Leveraging phylogenetic signal to unravel microbial community function and assembly rules
Science Score: 57.0%
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○Scientific vocabulary similarity
Low similarity (5.2%) to scientific vocabulary
Repository
Code for: Leveraging phylogenetic signal to unravel microbial community function and assembly rules
Basic Info
- Host: GitHub
- Owner: silvtal
- Language: R
- Default Branch: main
- Size: 6.93 MB
Statistics
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
This repository includes the custom packages and scripts used in "Leveraging phylogenetic signal to unravel microbial community function and assembly rules" by Talavera-Marcos, Parras-Moltó and Aguirre de Cárcer (https://doi.org/10.21203/rs.3.rs-2272005/v1)
The approaches used for each section of the paper are listed down below
Folders and repositories for each section
- PCGs in the environment: BacterialCore.py
- Experimental dataset processing: 16S
- Mapping 16S sequences to genomes and metabolic modeling: TFM
- Core pangenome exploration: getcorereactions
- Drift modeling:
- Interactions between populations: Correlation graphs
Additional repositories
- outliers_search.R (generates Suppl. Fig. 4)
- Plotting FBA fluxes (Fig. 3 and Suppl. Fig. 2): SBMLtograph
Owner
- Name: Silvia Talavera Marcos
- Login: silvtal
- Kind: user
- Website: https://silvtal.github.io/
- Twitter: silvtal
- Repositories: 2
- Profile: https://github.com/silvtal
Biochemistry graduate. Bioinformatics MSc. PhD student. Interested in genomics, microbiology and health.
Citation (CITATION.cff)
cff-version: 1.2.0
message: "Original publication"
authors:
- family-names: Talavera-Marcos
given-names: Silvia
orcid: https://orcid.org/0000-0002-6923-2876
- family-names: Parras
given-names: Marcos
orcid: https://orcid.org/0000-0003-0529-627X
- family-names: Aguirre de Cárcer
given-names: Daniel
orcid: https://orcid.org/0000-0003-1104-9566
title: "Leveraging phylogenetic signal to unravel microbial community function and assembly rules"
version: 0
doi: 10.21203/rs.3.rs-2272005/v1
date-released: 2022-12-08