allydunham

aa_subtypes

Code for the MSB publication: Exploring amino acid functions and positional subtypes in a deep mutational landscape

cambridge_thesis_template

LaTeX PhD Thesis Template for the University of Cambridge.

deepscanscape

R package for annotating deep mutational scanning data using the deep mutational landscape

dms_mutations

Preliminary analysis of a combined DMS dataset, including clustering and VEP benchmark

foldx_interface_ddg

Pipeline allowing parallel computation of protein interface mutation Gibbs Free Energy changes.

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

proteinnetpy

A python library for working with ProteinNet data

sequence_unet

Fully convolutional deep learning variant effect predictor architecture

tblhelpr

Helper functions for common opperations on Tidyverse Tibbles

allydunham/sequence_unet

Fully convolutional deep learning variant effect predictor architecture

allydunham/aa_subtypes

Code for the MSB publication: Exploring amino acid functions and positional subtypes in a deep mutational landscape

allydunham/deepscanscape

R package for annotating deep mutational scanning data using the deep mutational landscape

allydunham/foldx_interface_ddg

Pipeline allowing parallel computation of protein interface mutation Gibbs Free Energy changes.

allydunham/proteinnetpy

A python library for working with ProteinNet data

allydunham/tblhelpr

Helper functions for common opperations on Tidyverse Tibbles

allydunham/dms_mutations

Preliminary analysis of a combined DMS dataset, including clustering and VEP benchmark

allydunham/mutfunc_sars_cov_2

Pipeline used to generate variant effect predictions for all possible SARS-CoV-2 substitutions

allydunham/cambridge_thesis_template

LaTeX PhD Thesis Template for the University of Cambridge.

allydunham/mutfunc_sars_cov_2_frontend

Mutfunc: SARS-CoV-2 frontend code

allydunham/plotlistr

Tools for working with lists of plots, including labelling plots with attributes and automated saving

allydunham/btm2018

Basic Teaching Module 2018

allydunham/count_reads_python

Count structured sequencing reads

allydunham/dotfiles

Configuration dot files

allydunham/hog_pathway

S. cerevisiae genotype to phenotype prediction

allydunham/jabref

Graphical Java application for managing BibTeX and biblatex (.bib) databases

allydunham/misc_tools

Various small helper bioinformatics scripts and modules

allydunham/QUANTS

allydunham/Structural-Variation

Structural Variation in Human Populations MPhill Project Code Repository

allydunham/user-documentation

User documentation of JabRef

allydunham/yeast_strains

Genotype to phenotype prediction using transcriptomics and proteomics data.