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 last month
• Illumina / PromoterAI
  ☆80Updated 4 months ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆52Updated this week
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆97Updated 7 months ago
• jzhoulab / puffin_manuscript
  ☆18Updated last year
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer link prediction
  ☆43Updated last month
• calico / borzoi-paper
  Analyses related to the Borzoi paper.
  ☆22Updated last month
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆33Updated 9 months ago
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆30Updated 9 months ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆85Updated last month
• 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
• mcvickerlab / GenVarLoader
  Dataloader for applying sequence models to personalized genomics
  ☆27Updated last week
• 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
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆80Updated last year
• 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
• kundajelab / DART-Eval
  ☆42Updated 3 months ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆109Updated 2 years ago
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 6 months ago
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆48Updated 2 weeks ago
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆23Updated 2 months ago
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆64Updated 6 months ago
• liu-bioinfo-lab / EPCOT
  ☆24Updated last year
• ketringjoni / SuPreMo
  Pipeline for generating reference and perturbed sequences for input into predictive models.
  ☆11Updated 11 months 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
• ni-lab / personalized-expression-benchmark
  Evaluating genomic sequence models for explaining personalized expression variation
  ☆19Updated last year
• ShenLab-Genomics / SpliceTransformer
  SpliceTransformer(SpTransformer) is a deep learning tool to predict tissue specific splicing site from pre-mRNA sequence
  ☆29Updated 11 months ago
• ychuest / Awesome-LLMs-meet-genomes
  Explore a comprehensive collection of basic theories, applications, papers, and best practices about Large Language Models (LLMs) in geno…
  ☆103Updated 2 months ago
• amberT15 / LLM_eval
  Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"
  ☆22Updated last year
• Genentech / regLM
  Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
  ☆48Updated last year