Alternatives and similar repositories for borzoi-pytorch

Users that are interested in borzoi-pytorch are comparing it to the libraries listed below

• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer link prediction
  ☆44Updated 3 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆100Updated 10 months ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆86Updated 3 months ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆34Updated 11 months ago
• kundajelab / DART-Eval
  ☆42Updated 5 months ago
• 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
• mostafavilabuw / EnformerAssessment
  ☆25Updated last year
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆59Updated 3 weeks ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆82Updated last year
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆53Updated 2 months ago
• calico / baskerville
  Machine learning methods for DNA sequence analysis.
  ☆57Updated 4 months ago
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 9 months ago
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆93Updated 10 months ago
• ni-lab / personalized-expression-benchmark
  Evaluating genomic sequence models for explaining personalized expression variation
  ☆19Updated 2 years ago
• calico / borzoi
  RNA-seq prediction with deep convolutional neural networks.
  ☆220Updated 4 months ago
• theislab / sc-pert
  Models and datasets for perturbational single-cell omics
  ☆172Updated 3 years ago
• 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 / chrombpnet
  Bias factorized, base-resolution deep learning models of chromatin accessibility (chromBPNet)
  ☆201Updated 4 months ago
• gagneurlab / scooby
  scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.
  ☆54Updated 2 months ago
• GET-Foundation / get_model
  A modular framework for multimodal cross-cell-type transcriptional regulation models
  ☆98Updated 5 months ago
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆25Updated 4 months ago
• jmschrei / tangermeme
  Biological sequence analysis for the modern age.
  ☆260Updated last month
• d-laub / basenji2-pytorch
  PyTorch implementation of Basenji2.
  ☆19Updated 8 months ago
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆32Updated 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 …
  ☆38Updated 9 months ago
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆100Updated 4 months ago
• czi-ai / transcriptformer
  ☆98Updated 2 months ago
• mcvickerlab / GenVarLoader
  Dataloader for applying sequence models to personalized genomics
  ☆27Updated this week
• Hughes-Genome-Group / deepC
  A neural network framework for predicting the Hi-C chromatin interactions from megabase scale DNA sequence
  ☆33Updated last year