Debora Marks Lab (@debbiemarkslab)
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Top repositories

1

EVcouplings

Evolutionary couplings from protein and RNA sequence alignments
Jupyter Notebook
189
star
2

DeepSequence

A generative latent variable model for biological sequence families.
Python
160
star
3

plmc

Inference of couplings in proteins and RNAs from sequence variation
C
98
star
4

SeqDesign

Protein design and variant prediction using autoregressive generative models
Python
65
star
5

EVmutation

Mutation effects predicted from sequence co-variation
HTML
45
star
6

EVzoom

Visually explore covariation in protein families
JavaScript
34
star
7

neural-fingerprint-theano

Visual Convolutional Neural Graph Fingerprints in Theano/Lasagne
HTML
32
star
8

variational-synthesis

Repository for the paper "Optimal design of stochastic DNA synthesis protocols based on generative sequence models" (Weinstein et al., AISTATS, 2022).
Python
25
star
9

NEMO

Learning protein structure with a differentiable simulator
Python
25
star
10

BEAR

This repository is for the paper "A generative nonparametric Bayesian model for whole genomes"
Python
12
star
11

MuE

A package for making MuE observation models in Edward2.
Python
12
star
12

3D_from_DMS_Extended_Data

Jupyter Notebook
10
star
13

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
8
star
14

persistent-vi

Variational Bayes for discrete undirected models
C
7
star
15

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
7
star
16

nanobody-polyreactivity

Polyreactivity Website
Python
6
star
17

GELMMnet

Generalized linear mixed model elastic net
Jupyter Notebook
3
star