abxrxpro

Visualise your isolate's antibiotic resistance profile

abxrxpro-legacy

atp-data-plot

Visualise ATP over time under antibiotic challenge from the literature

atpscan

Analysis tools used for scanning ATP production in my E. coli UTI89 model in ScrumPy

caileancarter

comparespecieslists

cpp-training

My training scripts for C++

ecolicollection

Scripts used for handling my E coli assemblies collection

embltofasta

Convert EMBL files to FASTA

enrichment-plot

Map gene presence/absence results as metabolic pathways

escher

Build, share, and embed visualizations of metabolic pathways.

ezclermont

Phylotype your strains using Clermont's 2013 method: ezclermont.org

fasta_from_ena

Download FASTA files from ENA using an XML report of a search.

fastafromblast

Extract FASTA sequences of regions of genome assemblies from NCBI BLAST alignments

gaussian-elimination

A training script for learning Gaussian elimination

gpa-plotter

Plot Roary gene presence/absence results

kmerfinder

lpscanner

Rapid linear programme scanning and batch processing for ScrumPy

mobilegeneticelementdatabase

Contains a fasta format database of a large variety of mobile genetic elements and an annotation file

rbh_tools

reambap

Remove ambiguous base pairs from FASTA files

scipy-2017-cython-tutorial

Material for the SciPy 2017 Cython tutorial

scrumpy-notebook

Learn metabolic modelling and using ScrumPy for modelling.

short-read-dilutions-calc

A script I use for quickly converting Qubit readings from DNA extractions into dilutions I need for submitting my samples for short read sequencing.

sparcc

SparCC is a Python module for calculating correlations in compositional data

st-literature-search

Literature search tool for publications relating to E. coli sequence types

tabular2fasta

tuakit

Toolkit from tuatara

tuatara

Reconstruct and handle many genome-scale metabolic models in ScrumPy

upec_pop_study_norfolk

Material for "UPEC Population Structure and Antimicrobial Susceptibility in Norfolk, UK"