bsmith89

StrainFacts

Factorize metagenotypes to infer strains and their abundances

StrainZip

Unified co-assembly and pseudo-alignment

gtpro-strain-factorization

Run StrainFacts on very large GT-PRO data

midas2-wiki

Auxiliary repo for developing the MIDAS2 documentation

pymc-examples

Examples of PyMC3 models, including a library of Jupyter notebooks.

strain-aware-assembly

Deconvolve strain-specific paths on an assembly graph.

strain-corr

Finding correlations between inferred strains and patient features.

StrainFacts-manuscript

Code and metadata for "Scalable microbial strain inference in metagenomic data using StrainFacts"

blog

compbio-container

dotfiles

Keep a clean ~/

resume

My CV and a template for future-proof resume building

StrainPGC

Strain-informed gene content inference using metagenomic data

asmbl-depth-smoothing

Heuristic algorithm to smooth noisy k-mer counts on a de Bruijn graph

blog-theme

Original theme for blog.byronjsmith.com

bsmith89.github.io

clustering-playground

Clustering tutorial inspired by H&H Chapter 5.

compbio-template2

A base template for computation biology projects.

fmt-mgen

gt-pro

haplo-benchmark

Benchmarking StrainFacts against other tools.

longev-mgen

Code and metadata for analysis of Muribaculaceae MAGs manuscript

micro.glmm

MIDAS2

Microbiome - Integrated Gut Genome

pymc3

Probabilistic Programming in Python. Uses Theano as a backend, supports NUTS and ADVI.

sc-validate-haplotypes

Validate StrainFacts inferences with "single-cell" (droplet based) bacterial genomic sequencing.

Smith2022-UCFMT

Code and metadata for Smith 2022 Paper

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

StrainPGC-manuscript

Manuscript associated with StrainPGC tool for gene content estimation