Silvia Talavera Marcos's repositories
TFM
Este repositorio recoge los scripts desarrollados para automatizar los análisis correspondientes al Trabajo de Fin de Máster "Modelización metabólica de comunidades microbianas estables crecidas con fuentes de carbono y energía únicas y simples" (Silvia Talavera Marcos, Máster en Bioinformática y Biología Computacional, Universidad Autónoma de Madrid).
correlation_graphs
Based on Goyal et al.'s recently published method for inferring statistically significant correlations between OTUs (https://www.biorxiv.org/content/10.1101/2021.01.04.425224v1)
custom_ot2_utils
Opentrons OT2 robot functions or custom labware definitions that we feel other people might find useful
SBML_to_graph
A few rudimentary functions to generate metabolite graphs from SBML models. Uses ReFramed and one CarveMe function.
carveme
CarveMe: genome-scale metabolic model reconstruction
cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:
eggnog-mapper
Fast genome-wide functional annotation through orthology assignment
get_core_reactions
Given a folder with eggnog annotation files (multiple genomes), create a consensus annotations file and save a series of core reactions in different formats
MicrobeAnnotator
Pipeline for metabolic annotation of microbial genomes
ntinfo
ntinfo includes functions similar to those of CUSP and the Reverse Complement online tool. This script also comes with a supplementary GUI (ntitk.py). Saved as a .lnk file, everything is just a click away (including help).
phyloassembly
Code for: Leveraging phylogenetic signal to unravel microbial community function and assembly rules
rstoolbox
Python Toolbox For Rosetta Silent Files Processing
silvtal.github.io
Personal website
spyder-cyberpunk-color-theme
A good old magenta+cyan cyberpunk theme for Python syntax coloring in Spyder
tnseq_read_simulation
Reads simulation and analysis following the alternative method proposed at https://journals.asm.org/doi/full/10.1128/mSystems.00976-20# (Fig 1, right)