Alternatives and similar repositories for HiCFoundation:

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

• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆85Updated 5 months ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆38Updated 4 months ago
• GET-Foundation / get_model
  A modular framework for multimodal cross-cell-type transcriptional regulation models
  ☆64Updated 3 weeks ago
• tianshilu / pMTnet
  Deep Learning the T Cell Receptor Binding Specificity of Neoantigen
  ☆78Updated 2 years ago
• arnavmdas / epiphany
  ☆10Updated last year
• BGIResearch / BioLLM
  ☆19Updated this week
• kundajelab / DART-Eval
  ☆32Updated this week
• amberT15 / LLM_eval
  Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"
  ☆18Updated 9 months ago
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆56Updated 2 months ago
• OmicsML / CellPLM
  Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.
  ☆78Updated last year
• jkobject / geneformer
  ☆57Updated last year
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆42Updated last week
• xCompass-AI / GeneCompass
  GeneCompass
  ☆72Updated 8 months ago
• dohlee / chromoformer
  The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
  ☆34Updated last year
• vandijklab / cell2sentence
  Cell2Sentence: Teaching Large Language Models the Language of Biology
  ☆45Updated 3 months ago
• aristoteleo / awesome-bioagent-papers
  Agent self-driven repository on bio-agent papers, i.e. papers on LLM-based agents in biology and medicine.
  ☆29Updated last week
• HelloWorldLTY / scEval
  Codes for paper: Evaluating the Utilities of Large Language Models in Single-cell Data Analysis.
  ☆64Updated 2 months ago
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆24Updated last week
• SuperBianC / scMulan
  Repository for paper scMulan: a multitask generative pre-trained language model for single-cell analysis.
  ☆57Updated 10 months ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆73Updated 8 months ago
• xiongxslab / Translatomer
  ☆18Updated last month
• liu-bioinfo-lab / EPCOT
  ☆21Updated last year
• theislab / nicheformer
  Repository for Nicheformer: a foundation model for single-cell and spatial omics
  ☆86Updated this week
• ychuest / Awesome-LLMs-meet-genomes
  Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in geno…
  ☆40Updated last week
• Perturbation-Response-Prediction / PRnet
  PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturb…
  ☆40Updated 3 months ago
• Genentech / polygraph
  Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …
  ☆28Updated 2 months ago
• ni-lab / personalized-expression-benchmark
  Evaluating genomic sequence models for explaining personalized expression variation
  ☆19Updated last year
• mostafavilabuw / EnformerAssessment
  ☆19Updated 7 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆93Updated 3 weeks ago
• epigen / CellWhisperer
  CellWhisperer bridges the gap between transcriptomics data and natural language, enabling intuitive interaction with scRNA-seq datasets
  ☆52Updated 5 months ago