Byron J. Smith's repositories
resume
My CV and a template for future-proof resume building
strain-corr
Finding correlations between inferred strains and patient features.
StrainPGC
Strain-informed gene content inference using metagenomic data
StrainFacts
Factorize metagenotypes to infer strains and their abundances
een-metagenomics
Metagenomics analysis code for https://doi.org/10.1101/2023.12.21.23300351
StrainPGC-manuscript
Manuscript associated with StrainPGC tool for gene content estimation
strain-aware-assembly
Deconvolve strain-specific paths on an assembly graph.
MIDAS2
Microbiome - Integrated Gut Genome
snakemake
This is the development home of the workflow management system Snakemake. For general information, see
StrainPanDA
A method for reconstruction of subspecies composition and functional profiles from metagenomic data
dotfiles
Keep a clean ~/
clustering-playground
Clustering tutorial inspired by H&H Chapter 5.
compbio-template2
A base template for computation biology projects.
midas2-wiki
Auxiliary repo for developing the MIDAS2 documentation
StrainFacts-manuscript
Code and metadata for "Scalable microbial strain inference in metagenomic data using StrainFacts"
Smith2022-UCFMT
Code and metadata for Smith 2022 Paper
sc-validate-haplotypes
Validate StrainFacts inferences with "single-cell" (droplet based) bacterial genomic sequencing.
haplo-benchmark
Benchmarking StrainFacts against other tools.
longev-mgen
Code and metadata for analysis of Muribaculaceae MAGs manuscript
gtpro-strain-factorization
Run StrainFacts on very large GT-PRO data
asmbl-depth-smoothing
Heuristic algorithm to smooth noisy k-mer counts on a de Bruijn graph
pymc-examples
Examples of PyMC3 models, including a library of Jupyter notebooks.
pymc3
Probabilistic Programming in Python. Uses Theano as a backend, supports NUTS and ADVI.