Alternatives and similar repositories for clipnet

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

• kundajelab / ProCapNet
  Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.
  ☆17Updated 4 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆100Updated 10 months ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆34Updated 11 months ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer link prediction
  ☆44Updated 3 months ago
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆32Updated 11 months ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆86Updated 3 months ago
• Illumina / PromoterAI
  ☆87Updated last month
• jzhoulab / puffin_manuscript
  ☆18Updated last year
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆53Updated 2 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆90Updated 2 months ago
• calico / borzoi-paper
  Analyses related to the Borzoi paper.
  ☆25Updated last month
• 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…
  ☆56Updated last week
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆111Updated 3 years ago
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆67Updated 9 months ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆82Updated 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…
  ☆72Updated 2 years ago
• kundajelab / DART-Eval
  ☆42Updated 5 months ago
• EngreitzLab / scE2G
  Pipeline to run scE2G
  ☆32Updated 2 months ago
• liu-bioinfo-lab / EPCOT
  ☆26Updated 2 years ago
• mostafavilabuw / EnformerAssessment
  ☆25Updated last year
• kundajelab / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆201Updated 4 months ago
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆25Updated 4 months ago
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆59Updated 3 weeks ago
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 9 months ago
• statbiophys / OLGA
  Compute generation probabilities of CDR3 amino acid and nucleotide sequences
  ☆63Updated last month
• ni-lab / personalized-expression-benchmark
  Evaluating genomic sequence models for explaining personalized expression variation
  ☆19Updated 2 years ago
• gagneurlab / scooby
  scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.
  ☆54Updated 2 months ago
• ketringjoni / SuPreMo
  Pipeline for generating reference and perturbed sequences for input into predictive models.
  ☆11Updated last year
• ychuest / Awesome-LLMs-meet-genomes
  Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in geno…
  ☆118Updated 3 weeks ago
• jmschrei / dragonnfruit
  A method for analyzing scATAC-seq experiments.
  ☆34Updated 6 months ago