yal054

yal054's Stars

• instadeepai/nucleotide-transformer

  🧬 Nucleotide Transformer: Building and Evaluating Robust Foundation Models for Human Genomics

  Language:Python42050

• drieslab/Giotto

  Spatial omics analysis toolbox

  Language:R24095

• vgteam/vg

  tools for working with genome variation graphs

  Language:C++1.1k191

• haowenz/chromap

  Fast alignment and preprocessing of chromatin profiles

  Language:C++18418

• jzhoulab/orca

  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale

  Language:Python7021

• Winnie09/GPTCelltype

  Language:HTML12718

• state-spaces/mamba

  Mamba SSM architecture

  Language:Python11.5k941

• alxndrTL/mamba.py

  A simple and efficient Mamba implementation in pure PyTorch and MLX.

  Language:Python77263

• evo-design/evo

  Biological foundation modeling from molecular to genome scale

  Language:Jupyter Notebook86799

• pachterlab/seqspec

  machine-readable file format for genomic library sequence and structure

  Language:Python10517

• mulinlab/CAUSALdb-finemapping-pip

  A GWAS fine-mapping pipeline used in CAUSALdb

  Language:Python244

• broadinstitute/infercnv

  Inferring CNV from Single-Cell RNA-Seq

  Language:R525158

• pk7zuva/Circle_finder

  Micro DNA identification

  Language:Shell2113

• bowang-lab/scGPT

  Language:Jupyter Notebook919166

• DeplanckeLab/ChromatinHD

  High-definition modeling of chromatin + transcriptomics data

  Language:Python16

• ernstlab/LECIF

  Learning a genome-wide score of conservation at the functional genomics level between human and mouse

  Language:Python121

• lucidrains/bit-diffusion

  Implementation of Bit Diffusion, Hinton's group's attempt at discrete denoising diffusion, in Pytorch

  Language:Python31718

• ML4GLand/EUGENe

  Elucidating the Utility of Genomic Elements with Neural Nets

  Language:Jupyter Notebook594

• Significant-Gravitas/AutoGPT

  AutoGPT is the vision of accessible AI for everyone, to use and to build on. Our mission is to provide the tools, so that you can focus on what matters.

  Language:Python164k43.4k

• kundajelab/chrombpnet

  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)

  Language:Jupyter Notebook10327

• microsoft/DeepSpeed

  DeepSpeed is a deep learning optimization library that makes distributed training and inference easy, efficient, and effective.

  Language:Python33.7k4k

• macs3-project/MACS

  MACS -- Model-based Analysis of ChIP-Seq

  Language:Cython691270

• Vizgen/vizgen-postprocessing

  Language:Python224

• pinellolab/DNA-Diffusion

  🧬 Generative modeling of regulatory DNA sequences with diffusion probabilistic models 💨

  Language:Jupyter Notebook35148

• hakyimlab/PrediXcan

  PrediXcan Project

  Language:Python10356

• Teichlab/scg_lib_structs

  Collections of library structure and sequence of popular single cell genomic methods

  Language:HTML39886

• chonyy/PageRank-HITS-SimRank

  🎏 Python implementation of link analysis algorithm.

  Language:Python7131

• FMInference/FlexGen

  Running large language models on a single GPU for throughput-oriented scenarios.

  Language:Python9.1k528

• morris-lab/CellOracle

  This is the alpha version of the CellOracle package

  Language:Python29049

• omerwe/polyfun

  PolyFun (POLYgenic FUNctionally-informed fine-mapping)

  Language:Python8220