Alternatives and similar repositories for polygraph:

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

• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆56Updated 2 months ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆38Updated 3 months ago
• Genentech / regLM
  Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
  ☆36Updated 5 months ago
• liu-bioinfo-lab / EPCOT
  ☆21Updated last year
• amberT15 / LLM_eval
  Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"
  ☆17Updated 8 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆40Updated last month
• mhorlacher / rbpnet
  ☆18Updated 11 months ago
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆29Updated last month
• kundajelab / DART-Eval
  ☆30Updated 2 weeks ago
• mcvickerlab / GenVarLoader
  Dataloader for applying sequence models to personalized genomics
  ☆22Updated this week
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆24Updated 5 months ago
• shtoneyan / gopher
  Toolset for training quantitative sequence to function models.
  ☆23Updated 11 months ago
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆47Updated 3 weeks ago
• MiraldiLab / maxATAC
  Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
  ☆27Updated last week
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆72Updated 8 months ago
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆12Updated this week
• ekernf01 / perturbation_benchmarking
  Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.
  ☆17Updated this week
• epigen / KPNN
  Knowledge-primed neural networks
  ☆35Updated last year
• GET-Foundation / get_model
  A modular framework for multimodal cross-cell-type transcriptional regulation models
  ☆61Updated last week
• aertslab / CREsted
  CREsted is a Python package for training sequence-based deep learning models on scATAC-seq data, for capturing enhancer code and for desi…
  ☆32Updated this week
• mostafavilabuw / EnformerAssessment
  ☆19Updated 6 months ago
• karbalayghareh / GraphReg
  Chromatin interaction aware gene regulatory modeling with graph attention networks
  ☆26Updated 2 years ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆27Updated last month
• autosome-ru / LegNet
  accurate prediction of promoter activity and variant effects from massive parallel reporter assays
  ☆35Updated 4 months ago
• theislab / prophet
  ☆29Updated 2 weeks ago
• jzhoulab / puffin_manuscript
  ☆17Updated 4 months ago
• ML4GLand / EUGENe
  Elucidating the Utility of Genomic Elements with Neural Nets
  ☆67Updated 3 months ago
• KarchinLab / mhcnuggets
  MHC Class I and Class II neoantigen binding prediction
  ☆28Updated last year
• ni-lab / personalized-expression-benchmark
  Evaluating genomic sequence models for explaining personalized expression variation
  ☆19Updated last year
• calico / baskerville
  Machine learning methods for DNA sequence analysis.
  ☆37Updated this week