Alternatives and similar repositories for EPCOT

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

• jzhoulab / puffin_manuscript
  ☆18Updated last year
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer link prediction
  ☆43Updated last month
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆64Updated 6 months ago
• ketringjoni / SuPreMo
  Pipeline for generating reference and perturbed sequences for input into predictive models.
  ☆11Updated 11 months ago
• visze / sequence_cnn_models
  ☆13Updated 9 months ago
• karbalayghareh / GraphReg
  Chromatin interaction aware gene regulatory modeling with graph attention networks
  ☆27Updated 2 years ago
• d-laub / basenji2-pytorch
  PyTorch implementation of Basenji2.
  ☆16Updated 5 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆79Updated last week
• mostafavilabuw / EnformerAssessment
  ☆24Updated last year
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆23Updated last month
• ma-compbio / Higashi
  single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, hypergraph
  ☆90Updated last year
• HelloWorldLTY / UKBioLM
  ☆21Updated 6 months ago
• mhorlacher / rbpnet
  ☆18Updated last year
• FunctionLab / sei-manuscript
  Code for reproducing the Sei manuscript results
  ☆17Updated 3 years ago
• xiongxslab / Translatomer
  ☆24Updated last month
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 6 months ago
• calico / borzoi-paper
  Analyses related to the Borzoi paper.
  ☆22Updated last month
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆30Updated 9 months ago
• dylkot / pyWNN
  Weighted Nearest Neighbors Analysis implemented in Python (pyWNN)
  ☆18Updated 4 years ago
• shtoneyan / gopher
  Toolset for training quantitative sequence to function models.
  ☆23Updated last year
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆80Updated last year
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆97Updated 7 months ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆109Updated 2 years ago
• Genentech / polygraph
  Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …
  ☆35Updated 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…
  ☆70Updated 2 years ago
• yal054 / epiformer
  ☆26Updated 6 months ago
• ni-lab / personalized-expression-benchmark
  Evaluating genomic sequence models for explaining personalized expression variation
  ☆19Updated last year
• zhoujt1994 / scHiCluster
  ☆68Updated 4 months ago
• madilabcode / scNET
  ☆54Updated 3 weeks ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆52Updated this week