Alternatives and similar repositories for BRAID:

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

• phbradley / TCRdock
  python tools for TCR:peptide-MHC modeling and analysis
  ☆75Updated last year
• Genentech / gReLU
  gReLU is a python library to train, interpret, and apply deep learning models to DNA sequences.
  ☆260Updated 3 weeks ago
• ntranoslab / esm-variants
  ☆73Updated last year
• OATML-Markslab / EVE
  Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…
  ☆169Updated last year
• evanpeikon / Bioinformatics_Toolkit
  A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessib…
  ☆213Updated 3 weeks ago
• idekerlab / DrugCell
  A visible neural network model for drug response prediction
  ☆141Updated last year
• broadinstitute / depmap_omics
  What you need to process the Quarterly DepMap-Omics releases from Terra
  ☆115Updated this week
• sidhomj / DeepTCR
  Deep Learning Methods for Parsing T-Cell Receptor Sequencing (TCRSeq) Data
  ☆118Updated 2 years ago
• bionumpy / bionumpy
  Python library for array programming on biological datasets. Documentation available at: https://bionumpy.github.io/bionumpy/
  ☆281Updated this week
• theislab / sc-pert
  Models and datasets for perturbational single-cell omics
  ☆154Updated 2 years ago
• evanpeikon / PPI_Network_Analysis
  Mapping DEGs to PPI Networks, Identifying Network Hubs and Highly Connected Proteins, and Simulating Genetic Circuits. An End-to-End DIY …
  ☆20Updated 3 months ago
• KosinskiLab / AlphaPulldown
  ☆269Updated last week
• saezlab / pypath
  Python module for prior knowledge integration. Builds databases of signaling pathways, enzyme-substrate interactions, complexes, annotat…
  ☆143Updated this week
• wukevin / tcr-bert
  Large language modeling applied to T-cell receptor (TCR) sequences.
  ☆53Updated 3 years ago
• pgmikhael / protgps
  ☆75Updated last month
• Multiomics-Analytics-Group / course_protein_language_modeling
  ☆34Updated 3 months ago
• ArcInstitute / arc-virtual-cell-atlas
  Arc Virtual Cell Atlas
  ☆273Updated last week
• multimeric / Unipressed
  Comprehensive Python client for the Uniprot REST API
  ☆49Updated 8 months ago
• openvax / mhcflurry
  Peptide-MHC I binding affinity prediction
  ☆203Updated last month
• snap-stanford / KGWAS
  KGWAS: novel genetics discovery enabled by massive functional genomics knowledge graph
  ☆65Updated last month
• alchemab / bcr-repertoire-papers
  Collection of papers related to BCR repertoire analyses
  ☆18Updated 3 years ago
• jkobject / geneformer
  ☆62Updated last year
• sanderlab / scPerturb
  scPerturb: A resource and a python/R tool for single-cell perturbation data
  ☆124Updated 2 months ago
• Perturbation-Response-Prediction / PRnet
  PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturb…
  ☆46Updated 4 months ago
• theislab / chemCPA
  Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
  ☆112Updated 3 months ago
• Genentech / scimilarity
  A unifying representation of single cell expression profiles that quantifies similarity between expression states and generalizes to repr…
  ☆185Updated 2 months ago
• songlab-cal / gpn
  Genomic Pre-trained Network
  ☆265Updated last month
• theislab / cpa
  The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell leve…
  ☆99Updated 8 months ago
• KarchinLab / bigmhc
  BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity
  ☆52Updated last year
• BIMSBbioinfo / compgen_course_2025_module3
  Compgen Course 2025, Module 3 Course Material, Multi-omics integration using deep learning
  ☆57Updated last month