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    29 repositories

    • bcr-allelic-inclusion

      Public
      Model code and data for BCR allelic inclusion paper
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

    • phylogpn

      Public
      Code for "A Phylogenetic Approach to Genomic Language Modeling"
      Jupyter Notebook
      •0•0•0•0•Updated Oct 29, 2024Oct 29, 2024

    • forward-equivalent-trees

      Public
      Efficiently simulating multi-type birth-death processes via forward-equivalent parameter mapping
      Jupyter Notebook
      •
      MIT License
      •0•0•1•0•Updated Oct 16, 2024Oct 16, 2024

    • gpn

      Public
      Genomic Pre-trained Network
      dnalanguage-modelvariant-effect-prediction
      Jupyter Notebook
      •
      MIT License
      •24•188•2•0•Updated Oct 10, 2024Oct 10, 2024

    • CherryML

      Public
      Scalable Maximum Likelihood Estimation of Phylogenetic Models
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•8•1•2•Updated Jun 19, 2024Jun 19, 2024

    • scquint

      Public
      Jupyter Notebook
      •
      MIT License
      •1•15•1•1•Updated May 31, 2024May 31, 2024

    • flinty

      Public
      A Simple and Flexible Test of Sample Exchangeability with Applications to Statistical Genomics
      bioinformaticshypothesis-testinggenome-analysisnon-parametric-statisticsexchangeability
      Python
      •1•2•0•0•Updated Feb 5, 2024Feb 5, 2024

    • StratPGS

      Public
      Performance Inflation and Perturbation Sensitivity of PGSs
      statistical-genetics
      R
      •0•0•0•0•Updated Feb 5, 2024Feb 5, 2024

    • CPT

      Public
      Cross-protein transfer learning for variant effect prediction
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•17•1•0•Updated Sep 13, 2023Sep 13, 2023

    • HiDENSEC

      Public
      Code for Tracing cancer evolution and heterogeneity using Hi-C
      Jupyter Notebook
      •0•2•0•0•Updated Sep 4, 2023Sep 4, 2023

    • swga2

      Public template
      Python
      •
      Other
      •2•13•5•0•Updated Jul 27, 2023Jul 27, 2023

    • epigenome_editing_2023

      Public
      Code for training and analyzing models from the epigenome editing paper Batra et al.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Feb 23, 2023Feb 23, 2023

    • StableFM

      Public
      Data and scripts for fine-mapping stability project
      R
      •0•0•0•0•Updated Feb 21, 2023Feb 21, 2023

    • tape

      Public
      Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
      benchmarkdeep-learningprotein-structurelanguage-modelingpytorchdatasetsemi-supervised-learningprotein-sequences
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •129•662•24•4•Updated Dec 11, 2022Dec 11, 2022

    • factored-attention

      Public
      This repository contains code for reproducing results in our paper Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention
      proteinpottsattention
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •9•56•0•0•Updated Sep 30, 2022Sep 30, 2022

    • MOCHIS

      Public
      One- and two-sample tests against general families of alternatives
      Mathematica
      •0•3•0•0•Updated Jul 22, 2022Jul 22, 2022

    • slip

      Public
      SLIP is a sandbox environment for engineering protein sequences with synthetic fitness functions.
      Python
      •9•0•0•0•Updated Jul 6, 2022Jul 6, 2022

    • slc22a5

      Public
      Variant effect prediction for SLC22A5 transporter gene using Potts models
      proteinpotts
      Jupyter Notebook
      •0•1•0•0•Updated May 9, 2022May 9, 2022

    • mogwai

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•25•3•0•Updated May 9, 2022May 9, 2022

    • fairseq

      Public
      Facebook AI Research Sequence-to-Sequence Toolkit written in Python.
      Python
      •
      MIT License
      •6.4k•0•0•0•Updated Apr 4, 2022Apr 4, 2022

    • scquint-analysis

      Public
      Python
      •2•6•0•0•Updated Mar 1, 2022Mar 1, 2022

    • rna-sieve

      Public
      A library for the deconvolution of bulk cell samples using single-cell RNA expression data.
      Mathematica
      •
      GNU General Public License v3.0
      •4•20•1•0•Updated Nov 3, 2021Nov 3, 2021

    • contact-geometry

      Public
      Python
      •
      MIT License
      •1•4•0•0•Updated Oct 24, 2021Oct 24, 2021

    • tape-neurips2019

      Public
      Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (DEPRECATED)
      benchmarkdeep-learningprotein-structurelanguage-modelingdatasetsemi-supervised-learningprotein-sequences
      Python
      •
      MIT License
      •34•118•9•0•Updated Aug 7, 2021Aug 7, 2021

    • EGGTART

      Public
      Extensive GUI gives TASEP realization in real-time.
      1•1•0•0•Updated May 10, 2021May 10, 2021

    • MultiCluster

      Public
      Software for three-way clustering of multi-tissue multi-individual gene expression data using semi-nonnegative tensor decomposition
      MATLAB
      •1•4•0•0•Updated Sep 18, 2020Sep 18, 2020

    • l-TASEP

      Public
      Mathematica
      •0•0•0•0•Updated Jan 11, 2020Jan 11, 2020

    • SGDP_IGHV_TRBV

      Public
      Clustered and filtered reads after mapping for the SImons Diversity Genome Project.
      2•0•0•0•Updated Feb 11, 2019Feb 11, 2019

    • songlab-cal.github.io

      Public
      0•0•0•0•Updated Jun 1, 2018Jun 1, 2018