Max Cummins's repositories
pipelord_old
A collection of Snakemake workflows used by the Djordjevic Genomics Lab
Bioinformatics
A repository aimed to orient the uninitiated!
Romanian-mcr-1-Escherichia-coli
A repository detailing the whole genome sequence analysis of a collection of Escherichia coli from Romania
abricateR
abricate combinator
plasmidmapR
A package for the mass calculation and visualisation of reference plasmid coverage within whole genome sequence datasets
AVC171
A repository for a manuscript about an Australian APEC carrying a hybrid virulence resistance plasmid
AVC96-Supplementary_data
A repository containing a genome assembly for a manuscript submission
Bacsort
a collection of scripts for organising bacterial genomes by species
BLASTlord
A script facilitating filtering of BLAST data
BLASTlord-snek
These lords were made for BLASTn, 'n' that's just what they'll do!
bonechook
A repository supporting a manuscript on Australian APEC
Citrobacter
A repository containing analysis and associated scripts for a manuscript on a collection of Citrobacter
custom_DBs
Extra databases for aribalord snakemake pipeline
datasharing
The Leek group guide to data sharing
enterolordDB
A database with manually curated metadata, phylogenetic data generated by enterobase and genotypic data for public and custom databases generated using abricate
ExData_Plotting1
Plotting Assignment 1 for Exploratory Data Analysis
Getting-and-Cleaning-Data
Final project for Getting and Cleaning Data course
Pangenomelord
A snakemake pipeline for running Prokka and Roary
Pelegri_et_al_2023
A repository containing supplementary scripts for data processing and visualisation in Pelegri et al, 2023
pipelord3
A newerer and betterer pipelord version featuring wrappers
ProgrammingAssignment2
Repository for Programming Assignment 2 for R Programming on Coursera
Shuvlord
These lords were made for shuvvin, 'n' that's just what they'll do!
snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see