allydunham's repositories
sequence_unet
Fully convolutional deep learning variant effect predictor architecture
aa_subtypes
Code for the MSB publication: Exploring amino acid functions and positional subtypes in a deep mutational landscape
deepscanscape
R package for annotating deep mutational scanning data using the deep mutational landscape
foldx_interface_ddg
Pipeline allowing parallel computation of protein interface mutation Gibbs Free Energy changes.
proteinnetpy
A python library for working with ProteinNet data
dms_mutations
Preliminary analysis of a combined DMS dataset, including clustering and VEP benchmark
mutfunc_sars_cov_2
Pipeline used to generate variant effect predictions for all possible SARS-CoV-2 substitutions
cambridge_thesis_template
LaTeX PhD Thesis Template for the University of Cambridge.
mutfunc_sars_cov_2_frontend
Mutfunc: SARS-CoV-2 frontend code
plotlistr
Tools for working with lists of plots, including labelling plots with attributes and automated saving
count_reads_python
Count structured sequencing reads
hog_pathway
S. cerevisiae genotype to phenotype prediction
jabref
Graphical Java application for managing BibTeX and biblatex (.bib) databases
misc_tools
Various small helper bioinformatics scripts and modules
Structural-Variation
Structural Variation in Human Populations MPhill Project Code Repository
user-documentation
User documentation of JabRef
yeast_strains
Genotype to phenotype prediction using transcriptomics and proteomics data.