Alternatives and similar repositories for enformer_fine_tuning

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

• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆64Updated 7 months ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer link prediction
  ☆43Updated last month
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆82Updated last month
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆98Updated 8 months ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆33Updated 9 months ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆109Updated 2 years ago
• kundajelab / DART-Eval
  ☆42Updated 3 months ago
• ni-lab / personalized-expression-benchmark
  Evaluating genomic sequence models for explaining personalized expression variation
  ☆19Updated last year
• d-laub / basenji2-pytorch
  PyTorch implementation of Basenji2.
  ☆16Updated 6 months ago
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆50Updated last week
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆52Updated 3 weeks ago
• liu-bioinfo-lab / EPCOT
  ☆24Updated 2 years ago
• mostafavilabuw / EnformerAssessment
  ☆24Updated last year
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆30Updated 9 months ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆85Updated last month
• Illumina / PromoterAI
  ☆80Updated 4 months ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆81Updated last year
• jzhoulab / puffin_manuscript
  ☆18Updated last year
• bernardo-de-almeida / DeepSTARR
  Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…
  ☆71Updated 2 years ago
• johli / aparent
  APA Regression Net - Predict and Engineer Alternative Polyadenylation
  ☆39Updated 4 years ago
• 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…
  ☆51Updated last week
• emmijokinen / TCRconv
  TCRconv is a deep learning model for predicting recognition between T cell receptors and epitopes. It uses protBERT embeddings for the TC…
  ☆25Updated 3 years ago
• ketringjoni / SuPreMo
  Pipeline for generating reference and perturbed sequences for input into predictive models.
  ☆11Updated last year
• Genentech / regLM
  Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
  ☆49Updated last year
• autosome-ru / LegNet
  accurate prediction of promoter activity and variant effects from massive parallel reporter assays
  ☆42Updated 4 months ago
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 7 months ago
• HelloWorldLTY / UKBioLM
  ☆22Updated 6 months ago
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆91Updated 2 weeks ago
• calico / borzoi-paper
  Analyses related to the Borzoi paper.
  ☆22Updated last month
• ekernf01 / perturbation_benchmarking
  Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.
  ☆21Updated 2 months ago