jwestrob

astra

pyHMMer-based sequence search and retrieval tool.

GOOSOS

GOOSOS: Get ribOsOmal proteinS from prOtein faStas

Clustering_Funtime

I'm trying to do some stuff with some kmer embeddings. Maybe I'll make a binning algorithm out of it?

Script_Toybox

A bunch of stuff I've made over time.

alt_code_finder

Finding alt-coded contigs in metagenomic data

CSV-Heatmap-Parser

I'm being a good CS student and storing my data.

divergence-metrics

Embedder

A nifty script to take contigs/scaffolds, turn them into kmer frequency vectors, then perform dimensionality reduction (and give you a nice picture).

ESPM_112L

Markdown guides for ESPM 112L lab

Metaxas

An under-construction pipeline for assembly of QC'd illumina metagenomic sequencing reads.

Fasta-QC

Basic functionality to edit low-quality MSAs for phylogenetic analysis; deprecated in favor of vcf2aln

generate_context_genbanks

Generating genbanks with annotations for use with Clinker.

jwestrob.github.io

A Jekyll version of the "Prologue" theme by HTML5 UP

jwestrob2.github.io

metabolic-hmms

HMM databases for microbial metabolic genes of environmental/biogeochemical importance.

Metadata-Curvefit

Creating low-degree polynomial features from medical metadata in R.

mothur

Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

prbmao

This is not my code! This is a rainmeter skin generator, coded in C++. Instructions for use can be found in GUIDE.jpg. I found this on reddit.com/r/rainmeter and when I looked for a link to it to share with one of my friends, I found that none of them worked, and it didn't seem to be available anywhere else. I thought I'd make it available here!

Synteny-Graphs

Finding pneumococcal insertion sequences by examining differing weights in preserved edges in synteny graphs.

Tree_Simulator

These are the files I used to simulate my tree at CCG using pyvolve, tested with iq-tree. See README for details.

Tutorials