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cherryml

Scalable Maximum Likelihood Estimation of Phylogenetic Models

contact-geometry

cpt

Cross-protein transfer learning for variant effect prediction

eggtart

Extensive GUI gives TASEP realization in real-time.

epigenome_editing_2023

Code for training and analyzing models from the epigenome editing paper Batra et al.

factored-attention

This repository contains code for reproducing results in our paper Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention

fairseq

Facebook AI Research Sequence-to-Sequence Toolkit written in Python.

flinty

A Simple and Flexible Test of Sample Exchangeability with Applications to Statistical Genomics

forward-equivalent-trees

Efficiently simulating multi-type birth-death processes via forward-equivalent parameter mapping

gpn

Genomic Pre-trained Network

hidensec

Code for Tracing cancer evolution and heterogeneity using Hi-C

l-tasep

mochis

One- and two-sample tests against general families of alternatives

mogwai

multicluster

Software for three-way clustering of multi-tissue multi-individual gene expression data using semi-nonnegative tensor decomposition

rna-sieve

A library for the deconvolution of bulk cell samples using single-cell RNA expression data.

scquint

scquint-analysis

sgdp_ighv_trbv

Clustered and filtered reads after mapping for the SImons Diversity Genome Project.

slc22a5

Variant effect prediction for SLC22A5 transporter gene using Potts models

slip

SLIP is a sandbox environment for engineering protein sequences with synthetic fitness functions.

songlab-cal.github.io

stablefm

Data and scripts for fine-mapping stability project

stratpgs

Performance Inflation and Perturbation Sensitivity of PGSs

swga2

tape

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

tape-neurips2019

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (DEPRECATED)