Alternatives and similar repositories for perturbation_benchmarking

Users that are interested in perturbation_benchmarking are comparing it to the libraries listed below

• Genentech / decima
  Decima is a Python library to train sequence models on single-cell RNA-seq data.
  ☆36Updated last week
• mcvickerlab / GenVarLoader
  Dataloader for applying sequence models to personalized genomics
  ☆25Updated this week
• emmijokinen / TCRconv
  TCRconv is a deep learning model for predicting recognition between T cell receptors and epitopes. It uses protBERT embeddings for the TC…
  ☆25Updated 2 years ago
• altoslabs / perturbench
  ☆25Updated 4 months ago
• mhorlacher / rbpnet
  ☆18Updated last year
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆48Updated 3 weeks ago
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆48Updated last month
• MaayanLab / archs4py
  Python package to load and query ARCHS4 data
  ☆22Updated 2 months ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆42Updated 5 months ago
• autosome-ru / LegNet
  accurate prediction of promoter activity and variant effects from massive parallel reporter assays
  ☆35Updated 2 weeks ago
• DeplanckeLab / ChromatinHD
  High-definition modeling of chromatin + transcriptomics data
  ☆23Updated last month
• karbalayghareh / GraphReg
  Chromatin interaction aware gene regulatory modeling with graph attention networks
  ☆26Updated 2 years ago
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆57Updated last month
• brineylab / grp-paper
  Code and data used in The Great Repertoire Project
  ☆30Updated 3 years ago
• DanHanh / scLinear
  ☆19Updated 9 months ago
• epigen / KPNN
  Knowledge-primed neural networks
  ☆36Updated 2 years ago
• jishnu-lab / SLIDE
  ☆26Updated last week
• crazyhottommy / Machine_learning_drug_discovery
  ☆27Updated last month
• p-koo / creme-nn
  https://www.biorxiv.org/content/10.1101/2023.07.03.547592v2
  ☆29Updated 3 months ago
• shirondru / enformer_fine_tuning
  For fine-tuning Enformer using paired WGS & gene expression data
  ☆14Updated this week
• kundajelab / DART-Eval
  ☆34Updated 2 weeks ago
• matsengrp / sumrep
  Summary statistics for repertoires
  ☆17Updated 2 years ago
• kundajelab / coessentiality
  Companion to "A genome-wide almanac of co-essential modules assigns function to uncharacterized genes" (https://doi.org/10.1101/827071)
  ☆27Updated 2 years ago
• shtoneyan / gopher
  Toolset for training quantitative sequence to function models.
  ☆23Updated last year
• FunctionLab / tapioca
  a framework for predicting global protein-protein interaction networks from dynamic mass spec data
  ☆24Updated last year
• cantinilab / HuMMuS
  Molecular interactions inference from single-cell multi-omics data
  ☆24Updated 3 weeks ago
• chenhcs / FRoGS
  Functional Embedding of Gene Signatures
  ☆43Updated last year
• theislab / tcellmatch
  ☆39Updated 4 years ago
• IEDB / TCRMatch
  ☆29Updated 5 months ago
• TuftsBCB / RegDiffusion
  Diffusion model for gene regulatory network inference.
  ☆18Updated last month