Cailean Carter's Projects
Visualise your isolate's antibiotic resistance profile
Visualise ATP over time under antibiotic challenge from the literature
Analysis tools used for scanning ATP production in my E. coli UTI89 model in ScrumPy
My training scripts for C++
Scripts used for handling my E coli assemblies collection
Convert EMBL files to FASTA
Map gene presence/absence results as metabolic pathways
Build, share, and embed visualizations of metabolic pathways.
Phylotype your strains using Clermont's 2013 method: ezclermont.org
Download FASTA files from ENA using an XML report of a search.
Extract FASTA sequences of regions of genome assemblies from NCBI BLAST alignments
A training script for learning Gaussian elimination
Plot Roary gene presence/absence results
Rapid linear programme scanning and batch processing for ScrumPy
Contains a fasta format database of a large variety of mobile genetic elements and an annotation file
Remove ambiguous base pairs from FASTA files
Material for the SciPy 2017 Cython tutorial
Learn metabolic modelling and using ScrumPy for modelling.
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 is a Python module for calculating correlations in compositional data
Literature search tool for publications relating to E. coli sequence types
Toolkit from tuatara
Reconstruct and handle many genome-scale metabolic models in ScrumPy
Material for "UPEC Population Structure and Antimicrobial Susceptibility in Norfolk, UK"