Cailean Carter's repositories
GPA-Plotter
Plot Roary gene presence/absence results
ST-literature-search
Literature search tool for publications relating to E. coli sequence types
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
EcoliCollection
Scripts used for handling my E coli assemblies collection
LPScanner
Rapid linear programme scanning and batch processing for ScrumPy
ScrumPy-Notebook
Learn metabolic modelling and using ScrumPy for modelling.
UPEC_pop_study_Norfolk
Material for "UPEC Population Structure and Antimicrobial Susceptibility in Norfolk, UK"
Cpp-Training
My training scripts for C++
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
MobileGeneticElementDatabase
Contains a fasta format database of a large variety of mobile genetic elements and an annotation file
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
VirtualMicrobe
Incomplete real-time metabolic modelling tool