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.
  ☆15Updated 2 months ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆48Updated last month
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆44Updated 9 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆71Updated last month
• jzhoulab / puffin_manuscript
  ☆17Updated 10 months ago
• Illumina / PromoterAI
  ☆70Updated 2 months ago
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆29Updated 7 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆97Updated 5 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…
  ☆66Updated 2 years ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆85Updated 2 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…
  ☆44Updated last week
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆31Updated 7 months ago
• calico / borzoi-paper
  Analyses related to the Borzoi paper.
  ☆18Updated 2 months ago
• mcvickerlab / GenVarLoader
  Dataloader for applying sequence models to personalized genomics
  ☆27Updated last week
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆60Updated 4 months ago
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 4 months ago
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆22Updated 3 months ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆108Updated 2 years ago
• altoslabs / perturbench
  ☆37Updated 3 months ago
• mostafavilabuw / EnformerAssessment
  ☆23Updated last year
• xiongxslab / Translatomer
  ☆23Updated 6 months ago
• ketringjoni / SuPreMo
  Pipeline for generating reference and perturbed sequences for input into predictive models.
  ☆11Updated 9 months ago
• gagneurlab / scooby
  scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.
  ☆30Updated 2 weeks ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆78Updated last year
• 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 2 years ago
• liu-bioinfo-lab / EPCOT
  ☆24Updated last year
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆44Updated 2 weeks ago
• ekernf01 / perturbation_benchmarking
  Comparing performance across many methodological dimensions among tools that predict RNA after TF knockdowns and overexpression.
  ☆19Updated last week
• Genentech / polygraph
  Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …
  ☆35Updated 5 months ago
• theislab / tcellmatch
  ☆40Updated 5 years ago