Alternatives and similar repositories for personalized-expression-benchmark:

Users that are interested in personalized-expression-benchmark are comparing it to the libraries listed below

• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆35Updated 3 months ago
• mostafavilabuw / EnformerAssessment
  ☆18Updated 6 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆38Updated last month
• d-laub / basenji2-pytorch
  PyTorch implementation of Basenji2.
  ☆15Updated last year
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆55Updated last month
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆11Updated 3 weeks ago
• kundajelab / DART-Eval
  ☆27Updated last month
• liu-bioinfo-lab / EPCOT
  ☆20Updated last year
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆24Updated 4 months ago
• mcvickerlab / GenVarLoader
  Dataloader for applying sequence models to personalized genomics
  ☆22Updated this week
• Genentech / polygraph
  Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …
  ☆28Updated last month
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆26Updated 3 weeks ago
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆97Updated 2 years ago
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆47Updated this week
• jzhoulab / puffin_manuscript
  ☆17Updated 4 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…
  ☆57Updated last year
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆93Updated 3 months ago
• shtoneyan / gopher
  Toolset for training quantitative sequence to function models.
  ☆21Updated 11 months ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆67Updated last week
• Genentech / regLM
  Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
  ☆36Updated 4 months ago
• ML4GLand / EUGENe
  Elucidating the Utility of Genomic Elements with Neural Nets
  ☆65Updated 2 months ago
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆70Updated 7 months ago
• mhorlacher / rbpnet
  ☆18Updated 11 months ago
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆36Updated last week
• Papatheodorou-Group / BENGAL
  Nextflow pipeline for cross-species integration and assessment of single cell RNA-seq datasets
  ☆36Updated 10 months ago
• calico / borzoi
  RNA-seq prediction with deep convolutional neural networks.
  ☆122Updated 2 months ago
• calico / baskerville
  Machine learning methods for DNA sequence analysis.
  ☆37Updated last week
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆28Updated last month
• FunctionLab / sei-manuscript
  Code for reproducing the Sei manuscript results
  ☆16Updated 3 years ago
• GET-Foundation / get_model
  A modular framework for multimodal cross-cell-type transcriptional regulation models
  ☆57Updated last week