Will Pitchers's Projects
Materials for Analyzing Next-Generation Sequencing (ANGUS) course.
A Vim color scheme.
Sample files to accompany the FT's Chart Doctor column
A simple cgMLST pipeline
A tool for downloading Core Genome MLST schemes for bacterial genomics for use with chewBBACA
Scripts and data for the analyses from Pitchers et al. 2014 "The potential influence of morphology on the evolutionary divergence of an acoustic signal."
The Leek group guide to data sharing
:dragon: :fly: Assemble bacterial isolate genomes from Nanopore reads
workbook for assembly of the *Paramormyrops kingsleyae* genome
Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)
Software Carpentry introduction to Git for novices.
🍻 Default formulae for the missing package manager for macOS
:beer::microscope: Scientific formulae for the Homebrew package manager
Lesson on Getting to Know Your Data for genomics
repo for my scripts folder
Lesson on data organization and project setup for genomics
With a file of isolate IDs as input, compile all results (abricate, kraken, mlst) into a single table and infer an NJ tree using the alignment-free Andi phylogenomic software.
Analysis scripts for Tack et al. 2014
Code and Data for Pitchers et. al. 2014
Software Carpentry introduction to R for novices using inflammation data.
This is an R Markdown Notebook to document an analysis of the iris dataset that is packaged with the base installation of R.
Tool for finding & ID-ing stx alleles
Software Carpentry introduction to the shell for novices.
CFSAN Shigella Typing Pipeline