Alternatives and similar repositories for EPInformer

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

• mostafavilabuw / EnformerAssessment
  ☆25Updated last year
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆92Updated 2 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆100Updated 11 months ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆82Updated last year
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆67Updated 10 months ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆87Updated 4 months ago
• gagneurlab / scooby
  scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.
  ☆54Updated 3 months ago
• liu-bioinfo-lab / EPCOT
  ☆26Updated 2 years ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆54Updated 2 weeks 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…
  ☆57Updated this week
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆91Updated 3 months ago
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆62Updated last week
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆111Updated 3 years ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆34Updated last year
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆26Updated 5 months ago
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆95Updated 11 months ago
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆100Updated 4 months ago
• ni-lab / personalized-expression-benchmark
  Evaluating genomic sequence models for explaining personalized expression variation
  ☆19Updated 2 years ago
• ketringjoni / SuPreMo
  Pipeline for generating reference and perturbed sequences for input into predictive models.
  ☆11Updated last year
• kundajelab / DART-Eval
  ☆42Updated last week
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 10 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…
  ☆72Updated 2 years ago
• shtoneyan / gopher
  Toolset for training quantitative sequence to function models.
  ☆23Updated last year
• Hughes-Genome-Group / deepC
  A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
  ☆33Updated 2 weeks ago
• jmschrei / dragonnfruit
  A method for analyzing scATAC-seq experiments.
  ☆34Updated 7 months ago
• EngreitzLab / scE2G
  Pipeline to run scE2G
  ☆32Updated this week
• ekernf01 / perturbation_benchmarking
  Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.
  ☆22Updated 4 months ago
• calico / borzoi-paper
  Analyses related to the Borzoi paper.
  ☆25Updated last month
• calico / baskerville
  Machine learning methods for DNA sequence analysis.
  ☆57Updated this week
• yal054 / epiformer
  ☆27Updated 9 months ago