Alternatives and similar repositories for polygraph

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

• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆68Updated last month
• mhorlacher / rbpnet
  ☆18Updated last year
• Illumina / PromoterAI
  ☆65Updated last month
• ML4GLand / EUGENe
  Elucidating the Utility of Genomic Elements with Neural Nets
  ☆70Updated 8 months ago
• ketringjoni / SuPreMo
  Pipeline for generating reference and perturbed sequences for input into predictive models.
  ☆11Updated 8 months ago
• amberT15 / LLM_eval
  Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"
  ☆20Updated last year
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆60Updated 4 months ago
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 4 months ago
• kundajelab / DART-Eval
  ☆36Updated last week
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆31Updated 6 months ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆44Updated 8 months ago
• epigen / KPNN
  Knowledge-primed neural networks
  ☆38Updated 2 years ago
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆29Updated 6 months ago
• bernardo-de-almeida / DeepSTARR
  Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…
  ☆64Updated 2 years ago
• calico / baskerville
  Machine learning methods for DNA sequence analysis.
  ☆51Updated 3 weeks ago
• karbalayghareh / GraphReg
  Chromatin interaction aware gene regulatory modeling with graph attention networks
  ☆27Updated 2 years ago
• Genentech / regLM
  Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
  ☆43Updated 10 months ago
• vagarwal87 / Xpresso
  Predicting gene expression levels from genomic sequences
  ☆53Updated 5 years ago
• xiongxslab / Translatomer
  ☆22Updated 5 months ago
• jzhoulab / puffin_manuscript
  ☆17Updated 9 months ago
• mcvickerlab / GenVarLoader
  Dataloader for applying sequence models to personalized genomics
  ☆27Updated last week
• ekernf01 / perturbation_benchmarking
  Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.
  ☆19Updated 4 months ago
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆19Updated 2 months ago
• goodarzilab / SwitchFinder
  ☆18Updated last year
• liu-bioinfo-lab / EPCOT
  ☆23Updated last year
• gagneurlab / scooby
  scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.
  ☆27Updated this week
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆83Updated last month
• vagarwal87 / saluki_paper
  Saluki, a method to predict mRNA half-lives from sequence
  ☆25Updated 2 years ago
• autosome-ru / LegNet
  accurate prediction of promoter activity and variant effects from massive parallel reporter assays
  ☆38Updated last month
• shtoneyan / gopher
  Toolset for training quantitative sequence to function models.
  ☆23Updated last year