debbiemarkslab/plmc

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Created almost 9 years ago
Updated almost 2 years ago

debbiemarkslab/plmc

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Inference of couplings in proteins and RNAs from sequence variation

EVcouplings

Evolutionary couplings from protein and RNA sequence alignments

Jupyter Notebook

DeepSequence

A generative latent variable model for biological sequence families.

SeqDesign

Protein design and variant prediction using autoregressive generative models

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

variational-synthesis

Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AISTATS, 2022).

NEMO

Learning protein structure with a differentiable simulator

BEAR

This repository is for the paper "A generative nonparametric Bayesian model for whole genomes"

MuE

A package for making MuE observation models in Edward2.

3D_from_DMS_Extended_Data

Jupyter Notebook

variants_pharmacogenes

This repository contains the code used to analyse data and produce figures for the manuscript "Genetic variation in human drug-related genes"

Jupyter Notebook

persistent-vi

Variational Bayes for discrete undirected models

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

Jupyter Notebook

nanobody-polyreactivity

Polyreactivity Website

GELMMnet

Generalized linear mixed model elastic net

Jupyter Notebook