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abricater

abricate combinator

apec-mgen-2018

A repository providing data and scripts for a 2018 publication in Microbial Genomics

apg-ohec-retro-m1

A repository containing supplementary scripts for data processing and visualisation in Watt and Cummins et al, 2024

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

bioawk

BWK awk modified for biological data

bioinformatics

A repository aimed to orient the uninitiated!

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

chooklord

Scripts supporting antarctic lake manuscript in development

citrobacter

A repository containing analysis and associated scripts for a manuscript on a collection of Citrobacter

custom_dbs

Extra databases for aribalord snakemake pipeline

datasciencecoursera

datasharing

The Leek group guide to data sharing

e_coli_customdb

A custom database of IS elements and AMR- and virulence-associated gene sequences

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

pipelord

A microbial genomic analysis pipeline used by the Djordjevic Lab

pipelord2_0

pipelord3

A newerer and betterer pipelord version featuring wrappers

pipelord_old

A collection of Snakemake workflows used by the Djordjevic Genomics Lab

plasmidmapr

A package for the mass calculation and visualisation of reference plasmid coverage within whole genome sequence datasets

programmingassignment2

Repository for Programming Assignment 2 for R Programming on Coursera

romanian-mcr-1-escherichia-coli

A repository detailing the whole genome sequence analysis of a collection of Escherichia coli from Romania

sg17-135

A repository containing scripts for the generation of figures within a publication on an XDR strain of Salmonella sourced from an Australian Gull