Pinned Repositories
Trait-based_analyses
These analyses use a three step approach to cluster highly similar amino acid sequences from multiple genomes as 'functional traits', annotates them via KEGG and generates matrices in R for ecological analyses.
MD
Metagenomic diversity index calculator and example .faa contig data.
Black_Queen_simulations
This R code is for setting up and executing differential equations that describe the growth and interaction of simplistic 'Bacteria' in bulk soil and rhizosphere environments.
BlackQueen_metaGs
KEGG_formatting
Python scripts to format KEGG/KO outputs to R friendly inputs.
Laser_Gas_flux_processing
R code to process large data sets produced by continuous laser-derived gas measurements.
MicroEcoStats
R code and dummy data sets for statistical methods applied to microbial ecology.
MicroNiche_Vignette
This vignette is a step-by-step guide of the theory, mathematics and applications of the R package 'MicroNiche'.
MiSeq_read_reorientation
A python script to reorient MiSeq amplicons that have been sequenced in a mixture of forward and reverse orientations.
Workshop_Oct2022
DamienFinn's Repositories
DamienFinn/Trait-based_analyses
These analyses use a three step approach to cluster highly similar amino acid sequences from multiple genomes as 'functional traits', annotates them via KEGG and generates matrices in R for ecological analyses.
DamienFinn/MD
Metagenomic diversity index calculator and example .faa contig data.
DamienFinn/Black_Queen_simulations
This R code is for setting up and executing differential equations that describe the growth and interaction of simplistic 'Bacteria' in bulk soil and rhizosphere environments.
DamienFinn/BlackQueen_metaGs
DamienFinn/KEGG_formatting
Python scripts to format KEGG/KO outputs to R friendly inputs.
DamienFinn/Laser_Gas_flux_processing
R code to process large data sets produced by continuous laser-derived gas measurements.
DamienFinn/MicroEcoStats
R code and dummy data sets for statistical methods applied to microbial ecology.
DamienFinn/MicroNiche_Vignette
This vignette is a step-by-step guide of the theory, mathematics and applications of the R package 'MicroNiche'.
DamienFinn/MiSeq_read_reorientation
A python script to reorient MiSeq amplicons that have been sequenced in a mixture of forward and reverse orientations.
DamienFinn/Workshop_Oct2022