Alternatives and similar repositories for EPInformer

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

• mostafavilabuw / EnformerAssessment
  ☆24Updated last year
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆79Updated last week
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆64Updated 6 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆97Updated 7 months ago
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆48Updated 2 weeks ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆52Updated this week
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆85Updated last month
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆80Updated last year
• liu-bioinfo-lab / EPCOT
  ☆24Updated last year
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆109Updated 2 years ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆33Updated 8 months ago
• kundajelab / DART-Eval
  ☆42Updated 3 months 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…
  ☆49Updated last week
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 6 months ago
• ni-lab / personalized-expression-benchmark
  Evaluating genomic sequence models for explaining personalized expression variation
  ☆19Updated last year
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆98Updated last month
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆90Updated 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…
  ☆70Updated 2 years ago
• EngreitzLab / scE2G
  Pipeline to run scE2G
  ☆29Updated 2 weeks ago
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆93Updated 7 months ago
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆23Updated last month
• shtoneyan / gopher
  Toolset for training quantitative sequence to function models.
  ☆23Updated last year
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆182Updated last month
• calico / baskerville
  Machine learning methods for DNA sequence analysis.
  ☆55Updated last month
• dylkot / pyWNN
  Weighted Nearest Neighbors Analysis implemented in Python (pyWNN)
  ☆18Updated 4 years ago
• altoslabs / perturbench
  ☆43Updated last week
• pinellolab / simba
  SIMBA: SIngle-cell eMBedding Along with features
  ☆63Updated last year
• mcvickerlab / GenVarLoader
  Dataloader for applying sequence models to personalized genomics
  ☆27Updated last week
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆30Updated 9 months ago
• cantinilab / scPRINT
  🏃 The go-to single-cell Foundation Model
  ☆112Updated 2 weeks ago