Alternatives and similar repositories for finetuning-enformer

Users that are interested in finetuning-enformer are comparing it to the libraries listed below

• kundajelab / DART-Eval
  ☆42Updated 4 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆87Updated 2 weeks ago
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆64Updated 7 months ago
• castillohair / paper-5utr-design
  Code for "Optimizing 5’UTRs for mRNA-delivered gene editing using deep learning"
  ☆23Updated last year
• wukevin / tcr-bert
  Large language modeling applied to T-cell receptor (TCR) sequences.
  ☆57Updated 3 years ago
• kipoi / kipoiseq
  Standard set of data-loaders for training and making predictions for DNA sequence-based models.
  ☆82Updated last year
• autosome-ru / LegNet
  accurate prediction of promoter activity and variant effects from massive parallel reporter assays
  ☆43Updated 4 months ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆34Updated 10 months ago
• pjsample / human_5utr_modeling
  Modeling of human 5′ UTRs enables the design of new sequences for target levels of translation and 5′ UTR variant prediction.
  ☆53Updated 6 years ago
• johli / scrambler
  Interpretation by Deep Generative Masking for Biological Sequences
  ☆37Updated 3 years ago
• dohlee / chromoformer
  The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
  ☆36Updated 2 years ago
• johli / seqprop
  Stochastic Sequence Propagation - A Keras Model for optimizing DNA, RNA and protein sequences based on a predictor
  ☆50Updated last year
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer link prediction
  ☆42Updated 2 months ago
• czi-ai / transcriptformer
  ☆93Updated 3 weeks ago
• 1edv / evolution
  This repository contains the code for our manuscript - 'The evolution, evolvability, and engineering gene regulatory DNA'
  ☆96Updated 2 years ago
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆23Updated 3 months ago
• GfellerLab / MixMHC2pred
  HLA-II ligand predictor.
  ☆45Updated 2 years ago
• theislab / cpa
  The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell leve…
  ☆119Updated last year
• calico / baskerville
  Machine learning methods for DNA sequence analysis.
  ☆57Updated 3 months ago
• jychen01 / PISTE
  ☆25Updated last year
• ni-lab / personalized-expression-benchmark
  Evaluating genomic sequence models for explaining personalized expression variation
  ☆19Updated last year
• Genentech / regLM
  Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
  ☆50Updated last year
• amberT15 / LLM_eval
  Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"
  ☆22Updated last year
• evanseitz / squid-nn
  surrogate quantitative interpretability for deepnets
  ☆24Updated 3 months ago
• epigen / KPNN
  Knowledge-primed neural networks
  ☆38Updated 2 years ago
• frederikkemarin / BEND
  Benchmarking DNA Language Models on Biologically Meaningful Tasks
  ☆127Updated last year
• ihh / bilby
  Jax code for functional genomics ML
  ☆14Updated 8 months ago
• Genentech / polygraph
  Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …
  ☆38Updated 8 months ago
• mostafavilabuw / EnformerAssessment
  ☆24Updated last year
• jisraeli / DeepBind
  Training and testing of DeepBind models.
  ☆100Updated 10 years ago