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
  ☆43Updated 7 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆61Updated last week
• d-laub / basenji2-pytorch
  PyTorch implementation of Basenji2.
  ☆15Updated last month
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆17Updated last month
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆60Updated 2 months ago
• mostafavilabuw / EnformerAssessment
  ☆23Updated 10 months ago
• liu-bioinfo-lab / EPCOT
  ☆22Updated last year
• kundajelab / DART-Eval
  ☆34Updated last month
• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆38Updated this week
• mcvickerlab / GenVarLoader
  Dataloader for applying sequence models to personalized genomics
  ☆26Updated 2 weeks ago
• amberT15 / LLM_eval
  Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"
  ☆19Updated last year
• calico / baskerville
  Machine learning methods for DNA sequence analysis.
  ☆48Updated last week
• Genentech / polygraph
  Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …
  ☆32Updated 2 months ago
• HelloWorldLTY / UKBioLM
  ☆18Updated 2 months ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆29Updated 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…
  ☆63Updated 2 years ago
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 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…
  ☆40Updated last week
• shtoneyan / gopher
  Toolset for training quantitative sequence to function models.
  ☆23Updated last year
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆94Updated 3 months ago
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆80Updated this week
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆44Updated last week
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆105Updated 2 years ago
• jzhoulab / puffin_manuscript
  ☆17Updated 8 months ago
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆29Updated 5 months ago
• jmschrei / dragonnfruit
  A method for analyzing scATAC-seq experiments.
  ☆31Updated this week
• theislab / CFGen
  ☆17Updated this week
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆97Updated 5 months ago
• EngreitzLab / gene_network_evaluation
  Evaluation framework for computationally inferred gene networks from single-cell data.
  ☆13Updated 5 months ago
• EngreitzLab / scE2G
  Pipeline to run scE2G
  ☆26Updated last week