bsmith89

Microbial Ecologist; Postdoc in the Pollard Lab at the Gladstone Institutes; Carpentries Instructor

The Gladstone InstitutesSan Francisco, CA

Pinned Repositories

blog
Language:Python0 3 00
compbio-container
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compbio-template
A project template for computational biology, especially bioinformatics
Language:Makefile7 3 91
make-bml
Make (build-tool) lesson at Bodega Marine Lab Workshop, February 2016
Language:CSS6 3 51
resume
My CV and a template for future-proof resume building
Language:Makefile0 3 00
snakemake-boise
Two hour Snakemake lesson for Boise Joint User Groups Meeting
Language:Python00
StrainFacts
Factorize metagenotypes to infer strains and their abundances
Language:Python11 3 141
StrainPGC
Strain-informed gene content inference using metagenomic data
Language:Python0 2 00
StrainZip
Unified co-assembly and pseudo-alignment
Language:Python70

bsmith89's Repositories

bsmith89/StrainFacts
Factorize metagenotypes to infer strains and their abundances
Language:Python11 3 141
bsmith89/StrainZip
Unified co-assembly and pseudo-alignment
Language:Python70
bsmith89/gtpro-strain-factorization
Run StrainFacts on very large GT-PRO data
Language:Jupyter Notebook1 3 0
bsmith89/midas2-wiki
Auxiliary repo for developing the MIDAS2 documentation
11
bsmith89/pymc-examples
Examples of PyMC3 models, including a library of Jupyter notebooks.
Language:Python1 2 0
bsmith89/strain-aware-assembly
Deconvolve strain-specific paths on an assembly graph.
Language:Jupyter Notebook1 2 0
bsmith89/strain-corr
Finding correlations between inferred strains and patient features.
Language:Jupyter Notebook1 3 0
bsmith89/StrainFacts-manuscript
Code and metadata for "Scalable microbial strain inference in metagenomic data using StrainFacts"
Language:Jupyter Notebook1 3 0
bsmith89/blog
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bsmith89/compbio-container
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bsmith89/dotfiles
Keep a clean ~/
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bsmith89/resume
My CV and a template for future-proof resume building
Language:Makefile0 3 00
bsmith89/StrainPGC
Strain-informed gene content inference using metagenomic data
Language:Python0 2 00
bsmith89/asmbl-depth-smoothing
Heuristic algorithm to smooth noisy k-mer counts on a de Bruijn graph
Language:Jupyter Notebook3 0
bsmith89/blog-theme
Original theme for blog.byronjsmith.com
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bsmith89/bsmith89.github.io
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bsmith89/clustering-playground
Clustering tutorial inspired by H&H Chapter 5.
Language:Jupyter Notebook2 0
bsmith89/compbio-template2
A base template for computation biology projects.
Language:Python2 0
bsmith89/fmt-mgen
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bsmith89/gt-pro
bsmith89/haplo-benchmark
Benchmarking StrainFacts against other tools.
Language:Python
bsmith89/longev-mgen
Code and metadata for analysis of Muribaculaceae MAGs manuscript
Language:Jupyter Notebook4 0
bsmith89/micro.glmm
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bsmith89/MIDAS2
Microbiome - Integrated Gut Genome
Language:Python2 0
bsmith89/pymc3
Probabilistic Programming in Python. Uses Theano as a backend, supports NUTS and ADVI.
Language:Python3 0
bsmith89/sc-validate-haplotypes
Validate StrainFacts inferences with "single-cell" (droplet based) bacterial genomic sequencing.
Language:Jupyter Notebook
bsmith89/Smith2022-UCFMT
Code and metadata for Smith 2022 Paper
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bsmith89/snakemake
This is the development home of the workflow management system Snakemake. For general information, see
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bsmith89/StrainPanDA
A method for reconstruction of subspecies composition and functional profiles from metagenomic data
bsmith89/StrainPGC-manuscript
Manuscript associated with StrainPGC tool for gene content estimation
Language:Jupyter Notebook