Alternatives and similar repositories for squid-nn:

Users that are interested in squid-nn are comparing it to the libraries listed below

• autosome-ru / LegNet
  accurate prediction of promoter activity and variant effects from massive parallel reporter assays
  ☆32Updated 2 months ago
• emmijokinen / TCRconv
  TCRconv is a deep learning model for predicting recognition between T cell receptors and epitopes. It uses protBERT embeddings for the TC…
  ☆23Updated 2 years ago
• FunctionLab / tapioca
  a framework for predicting global protein-protein interaction networks from dynamic mass spec data
  ☆23Updated 10 months ago
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆51Updated last week
• johli / scrambler
  Interpretation by Deep Generative Masking for Biological Sequences
  ☆37Updated 3 years ago
• chenhcs / FRoGS
  Functional Embedding of Gene Signatures
  ☆39Updated 10 months ago
• mhorlacher / rbpnet
  ☆17Updated 9 months ago
• pinellolab / EPInformer
  code to run EPInformer for gene expression prediction and gene-enhancer links prioritization
  ☆34Updated last month
• kundajelab / DART-Eval
  ☆23Updated 3 weeks ago
• wukevin / tcr-bert
  Large language modeling applied to T-cell receptor (TCR) sequences.
  ☆48Updated 2 years ago
• NKI-AI / STAPLER
  STAPLER (Shared TCR And Peptide Language bidirectional Encoder Representations from transformers) is a language model that uses a joint T…
  ☆25Updated 8 months ago
• wassermanlab / ExplaiNN
  ExplaiNN: interpretable and transparent neural networks for genomics
  ☆45Updated last year
• Genentech / polygraph
  Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …
  ☆28Updated last week
• PaccMann / TITAN
  Code for "T Cell Receptor Specificity Prediction with Bimodal Attention Networks" (https://doi.org/10.1093/bioinformatics/btab294, ISMB 2…
  ☆29Updated last year
• epigen / KPNN
  Knowledge-primed neural networks
  ☆35Updated last year
• ntranoslab / esm-variants
  ☆69Updated last year
• pmoris / ImRex
  Generic TCR-epitope recognition prediction using CNN approach on both known and novel epitopes
  ☆15Updated last year
• dohlee / chromoformer
  The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
  ☆34Updated last year
• krishnanlab / obnb
  A Python toolkit for setting up benchmarking dataset using biomedical networks
  ☆21Updated 3 weeks ago
• xiongxslab / Translatomer
  ☆16Updated last month
• KarchinLab / bigmhc
  BigMHC predicts MHC-I (neo)epitope presentation and immunogenicity
  ☆48Updated 8 months ago
• bioinformatics-sannio / ncrna-deep
  Scripts and datasets to reproduce the experiment of the paper "Exploring non-coding RNA functions with deep learning tools"
  ☆13Updated 3 years ago
• antigenomics / tcren-ms
  📝 [Paper] TCRen: predicting TCR-peptide recognition based on residue-level pairwise statistical potential
  ☆15Updated last week
• GET-Foundation / get_model
  A modular framework for multimodal cross-cell-type transcriptional regulation models
  ☆35Updated this week
• tianshilu / pMTnet
  Deep Learning the T Cell Receptor Binding Specificity of Neoantigen
  ☆78Updated 2 years ago
• welch-lab / PerturbNet
  PerturbNet is a deep generative model that can predict the distribution of cell states induced by chemical or genetic perturbation
  ☆28Updated 2 months ago
• ctokheim / deepDegron
  Deep learning model to predict degron sequences
  ☆19Updated last year
• GreiffLab / immuneSIM
  ☆38Updated last year
• viragbioinfo / IMMREP_2022_TCRSpecificity
  ☆19Updated 2 years ago
• alchemab / bcr-repertoire-papers
  Collection of papers related to BCR repertoire analyses
  ☆17Updated 2 years ago