Alternatives and similar repositories for state

Users that are interested in state are comparing it to the libraries listed below

• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆60Updated 2 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆61Updated last week
• kundajelab / DART-Eval
  ☆34Updated last month
• bowang-lab / Orthrus
  Orthrus is a mature RNA model for RNA property prediction. It uses a mamba encoder backbone, a variant of state-space models specifical…
  ☆66Updated 5 months ago
• phbradley / TCRdock
  python tools for TCR:peptide-MHC modeling and analysis
  ☆79Updated last year
• Genentech / polygraph
  Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …
  ☆32Updated 2 months ago
• tianshilu / pMTnet
  Deep Learning the T Cell Receptor Binding Specificity of Neoantigen
  ☆81Updated 3 years ago
• theislab / CellFlow
  Modeling complex perturbations with CellFlow
  ☆57Updated this week
• Genentech / SpatialAgent
  ☆114Updated 2 months ago
• wukevin / tcr-bert
  Large language modeling applied to T-cell receptor (TCR) sequences.
  ☆53Updated 3 years ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆43Updated 7 months ago
• ychuest / Awesome-LLMs-meet-genomes
  Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in geno…
  ☆62Updated last week
• ntranoslab / esm-variants
  ☆74Updated last year
• HelloWorldLTY / scEval
  Codes for paper: Evaluating the Utilities of Large Language Models in Single-cell Data Analysis.
  ☆70Updated last week
• Genentech / iterative-perturb-seq
  Sequential Optimal Experimental Design of Perturbation Screens Guided by Multimodal Priors
  ☆40Updated last year
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆38Updated this week
• pmoris / ImRex
  Generic TCR-epitope recognition prediction using CNN approach on both known and novel epitopes
  ☆16Updated 2 years ago
• aaronwtr / PertEval
  Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.
  ☆26Updated 2 months ago
• KarchinLab / bigmhc
  BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity
  ☆53Updated last year
• Genentech / regLM
  Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
  ☆42Updated 8 months ago
• snap-stanford / KGWAS
  KGWAS: novel genetics discovery enabled by massive functional genomics knowledge graph
  ☆70Updated 3 months ago
• theislab / prophet
  ☆34Updated last month
• amberT15 / LLM_eval
  Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"
  ☆19Updated last year
• a96123155 / UTR-LM
  ☆88Updated 8 months ago
• czi-ai / transcriptformer
  ☆51Updated 2 weeks ago
• microsoft / zero-shot-scfoundation
  ☆66Updated 10 months ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆29Updated 4 months ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆75Updated 11 months ago
• jkobject / geneformer
  ☆69Updated last month
• dohlee / chromoformer
  The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
  ☆36Updated last year