Pinned Repositories
DeepSequence
A generative latent variable model for biological sequence families.
EVcouplings
Evolutionary couplings from protein and RNA sequence alignments
EVE
Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning"
EVEscape
Official repository for the paper "Learning from pre-pandemic data to forecast viral antibody escape"
EVmutation
Mutation effects predicted from sequence co-variation
EVzoom
Visually explore covariation in protein families
neural-fingerprint-theano
Visual Convolutional Neural Graph Fingerprints in Theano/Lasagne
plmc
Inference of couplings in proteins and RNAs from sequence variation
SeqDesign
Protein design and variant prediction using autoregressive generative models
variational-synthesis
Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AISTATS, 2022).
Debora Marks Lab's Repositories
debbiemarkslab/EVcouplings
Evolutionary couplings from protein and RNA sequence alignments
debbiemarkslab/DeepSequence
A generative latent variable model for biological sequence families.
debbiemarkslab/plmc
Inference of couplings in proteins and RNAs from sequence variation
debbiemarkslab/SeqDesign
Protein design and variant prediction using autoregressive generative models
debbiemarkslab/EVmutation
Mutation effects predicted from sequence co-variation
debbiemarkslab/EVzoom
Visually explore covariation in protein families
debbiemarkslab/neural-fingerprint-theano
Visual Convolutional Neural Graph Fingerprints in Theano/Lasagne
debbiemarkslab/variational-synthesis
Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AISTATS, 2022).
debbiemarkslab/NEMO
Learning protein structure with a differentiable simulator
debbiemarkslab/MuE
A package for making MuE observation models in Edward2.
debbiemarkslab/BEAR
This repository is for the paper "A generative nonparametric Bayesian model for whole genomes"
debbiemarkslab/popEVE
debbiemarkslab/3D_from_DMS_Extended_Data
debbiemarkslab/nanobody-polyreactivity
Polyreactivity Website
debbiemarkslab/variants_pharmacogenes
This repository contains the code used to analyse data and produce figures for the manuscript "Genetic variation in human drug-related genes"
debbiemarkslab/persistent-vi
Variational Bayes for discrete undirected models
debbiemarkslab/EVE
Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning"
debbiemarkslab/detectDesign
toolkit for finding likely cas9 off-target binding and effect on gene expression, designing sgRNAs and pairs of sgRNAs with minimal off-target effect on gene-expression
debbiemarkslab/GELMMnet
Generalized linear mixed model elastic net
debbiemarkslab/Vax_design
debbiemarkslab/EVEscape
Official repository for the paper "Learning from pre-pandemic data to forecast viral antibody escape"
debbiemarkslab/EVdeimmunization
Dual optimization of de-immunization and protein function
debbiemarkslab/edward2
A fork of Edward2, for use with the MuE package.
debbiemarkslab/GerA-suppData-2021
debbiemarkslab/sequenceMDS
debbiemarkslab/ZIP_benchmark