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 link prediction
  ☆42Updated 2 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆88Updated 3 weeks ago
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆23Updated 3 months ago
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆65Updated 8 months ago
• d-laub / basenji2-pytorch
  PyTorch implementation of Basenji2.
  ☆18Updated 7 months ago
• mostafavilabuw / EnformerAssessment
  ☆25Updated last year
• liu-bioinfo-lab / EPCOT
  ☆25Updated 2 years ago
• kundajelab / DART-Eval
  ☆42Updated 4 months ago
• jzhoulab / puffin
  deep learning-inspired explainable sequence model for transcription initiation
  ☆99Updated 9 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 8 months ago
• calico / baskerville
  Machine learning methods for DNA sequence analysis.
  ☆57Updated 3 months ago
• songlab-cal / TraitGym
  ☆14Updated last week
• FunctionLab / sei-framework
  code to run sei and obtain sei and sequence class predictions
  ☆109Updated 2 years ago
• calico / borzoi
  RNA-seq prediction with deep convolutional neural networks.
  ☆211Updated 3 months ago
• de-Boer-Lab / random-promoter-dream-challenge-2022
  ☆34Updated 10 months ago
• amberT15 / LLM_eval
  Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"
  ☆23Updated last year
• Genentech / regLM
  Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
  ☆50Updated last year
• jmschrei / tfmodisco-lite
  A lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments.
  ☆86Updated 2 months ago
• HelloWorldLTY / UKBioLM
  ☆22Updated 7 months ago
• calico / borzoi-paper
  Analyses related to the Borzoi paper.
  ☆23Updated 2 months ago
• Danko-Lab / clipnet
  A deep learning approach to predicting transcription initiation from sequence at single nucleotide resolution
  ☆14Updated 2 weeks ago
• bernardo-de-almeida / DeepSTARR
  Deep learning model built to quantitatively predict the activities of developmental and housekeeping enhancers from DNA sequence in Droso…
  ☆71Updated 2 years ago
• jzhoulab / puffin_manuscript
  ☆18Updated last year
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆32Updated 10 months ago
• ketringjoni / SuPreMo
  Pipeline for generating reference and perturbed sequences for input into predictive models.
  ☆11Updated last year
• jmschrei / bpnet-lite
  This repository hosts a minimal version of a Python API for BPNet.
  ☆53Updated last month
• tanjimin / C.Origami
  C.Origami, a prediction and screening framework for cell type-specific 3D chromatin structure.
  ☆82Updated last year
• calico / scBasset
  Sequence-based Modeling of single-cell ATAC-seq using Convolutional Neural Networks.
  ☆98Updated 3 months ago
• jzhoulab / orca
  sequence-based prediction of multiscale genome structure from kilobase to whole-chromosome scale
  ☆92Updated 9 months ago
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆49Updated 8 months ago