Discover debbiemarkslab/variants_pharmacogenes Open Source project

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debbiemarkslab

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

EVcouplings

Evolutionary couplings from protein and RNA sequence alignments

Jupyter Notebook

189

DeepSequence

A generative latent variable model for biological sequence families.

Python

160

plmc

Inference of couplings in proteins and RNAs from sequence variation

SeqDesign

Protein design and variant prediction using autoregressive generative models

Python

EVmutation

Mutation effects predicted from sequence co-variation

HTML

EVzoom

Visually explore covariation in protein families

JavaScript

neural-fingerprint-theano

Visual Convolutional Neural Graph Fingerprints in Theano/Lasagne

HTML

variational-synthesis

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

Python

NEMO

Learning protein structure with a differentiable simulator

Python

BEAR

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

Python

MuE

A package for making MuE observation models in Edward2.

Python

3D_from_DMS_Extended_Data

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

Python

GELMMnet

Generalized linear mixed model elastic net

Jupyter Notebook

debbiemarkslab/variants_pharmacogenes

debbiemarkslab

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