Computational Biology
371 items from inoue0426/awesome-computational-biology ★159
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CASSIA github.com
Multi-agent LLM framework for reference-free and interpretable single-cell cell-type annotation with dedicated annotation, validation, scoring, and reporting agents.
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biolord github.com
Deep generative model that disentangles known and unknown attributes for conditional generation of single-cell states.
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DeepSpot github.com
Deep learning model predicting spatial transcriptomics from H&E images at spot and single-cell resolution.
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CaSpER github.com
CNV identification and visualization by integrative analysis of single-cell or bulk RNA-seq data.
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PRNet github.com
Deep generative model for predicting transcriptional responses to novel chemical perturbations for drug discovery.
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ChemFM github.com
1B/3B-parameter chemical language model pretrained on 178M molecules for molecular representation, property prediction, generation, and synthesis tasks.
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BulkFormer github.com
Foundation model for bulk RNA-seq data; learns general transcriptomic representations.
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CpGPT github.com
DNA methylation foundation model pretrained on >150K samples for zero-shot imputation, array conversion, reference mapping, and downstream phenotype prediction.
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NeoDTI github.com
Library for drug-target interaction prediction.
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MIDAS github.com
Mosaic integration and differential accessibility model for single-cell multi-omics that handles arbitrary missing-modality combinations across transcriptomics, chromatin accessibility, and proteomics.
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EpiAgent github.com
scATAC-seq foundation model pretrained on ~5M cells and >35B tokens for representation learning, annotation, imputation, perturbation prediction, and in-silico cCRE knockout.
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MIRA github.com
Probabilistic multimodal topic model jointly modeling single-cell transcriptomics and chromatin accessibility for regulatory network inference.
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PerturbNet github.com
Conditional generative model for predicting distributions of single-cell states under unseen chemical and genetic perturbations.
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MethylGPT github.com
Transformer foundation model for DNA methylation pretrained on >150K human methylomes across thousands of datasets, with 3M/7M/15M parameter variants.
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scMulan github.com
Single-cell multi-omic language model pretrained on ~10M cells spanning transcriptomics, epigenomics, and proteomics for cross-omics transfer tasks.
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BRAD github.com
Retrieval-augmented bioinformatics assistant integrating scientific literature, databases, external tools, and executable workflows.
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TIGON github.com
Neural optimal transport method for reconstructing growth and dynamic trajectories from single-cell transcriptomics.
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DeepSpot-M github.com
Multimodal foundation model for transcriptome-wide virtual spatial transcriptomics from histology.
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STAGATE github.com
Adaptive graph attention auto-encoder for spatial domain identification in spatial transcriptomics.
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LPM github.com
Large perturbation model that jointly learns heterogeneous perturbation experiments by disentangling perturbation, readout, and context representations.
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BABEL github.com
Cross-modality translation model enabling prediction between scRNA-seq and scATAC-seq profiles without requiring paired single-cell measurements.
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UnitedNet github.com
Interpretable multi-task deep neural network for single-cell multi-omics integration spanning transcriptomics, chromatin accessibility, and proteomics.
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TxPert github.com
Knowledge-graph-informed latent-transfer model for transcriptomic perturbation prediction across unseen single perturbations, combinations, and cross-context settings.
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AutoZyme github.com
Autonomous agentic framework that speeds up bioinformatics software (e.g. Scanpy, Seurat) on CPUs while preserving the original results.
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BioAgents github.com
Multi-agent bioinformatics assistant using specialized language models and retrieval for genomics workflow development and troubleshooting.
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BIA github.com
Bioinformatics agent for GEO search, sample metadata extraction, count-matrix processing, and pipeline extraction from papers.
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ChatSpatial github.com
MCP server for spatial transcriptomics analysis via natural language.
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Prophet github.com
Transformer model for predicting cellular phenotypes under unseen chemical or genetic perturbations across heterogeneous assays and contexts.
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Concerto github.com
Contrastive self-supervised learning framework for single-cell multimodal data integration, batch correction, and reference-query mapping.
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GenBio-PathFM github.com
1.1B-parameter histopathology foundation model trained on public data using morphology-aware curation and dual-stage JEPA+DINO learning.
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scPRINT-2 github.com
Next-generation single-cell foundation model pretrained on 350M+ cells across 22K+ datasets and 16 species for embeddings, denoising, annotation, gene-network inference, and cross-species transfer.
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TranSiGen github.com
Dual-VAE architecture for ligand-based virtual screening, drug response prediction, and drug repurposing using chemical-induced transcriptional profiles.
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Matcha github.com
Multi-stage Riemannian flow matching model for physically valid molecular docking with scoring, pose filtering, and benchmarks.
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Multigrate github.com
Asymmetric multi-omics variational autoencoder for integrating single-cell data across RNA, ATAC, and protein modalities with missing-modality support.
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CancerFoundation github.com
Single-cell RNA-seq foundation model trained exclusively on a curated dataset of malignant cells to learn cancer-specific embeddings.
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DeepTalk github.com
Graph attention network for deciphering cell-cell communication from spatial transcriptomics.
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scButterfly github.com
Dual-aligned variational autoencoder for single-cell cross-modality translation between paired and unpaired multiomics data.
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AESTETIK github.com
Autoencoder for spatial transcriptomics representation learning using topology and histology image knowledge.
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XPert github.com
Knowledge-informed dual-branch Transformer for drug-induced transcriptional perturbation prediction across dose, time, and cellular context.
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RECOVER github.com
Machine learning framework for predicting synergistic drug combination responses across cell lines.
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CMonge github.com
Conditional optimal transport model for generalizable single-cell perturbation response prediction across drugs and doses.
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TGSA github.com
Tumor gene set and attention-based model leveraging biological pathway knowledge for drug response prediction.
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DeepSpot2Cell github.com
Predicts virtual single-cell spatial transcriptomics from H&E using spot-level supervision (NeurIPS 2025 Imageomics).
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scDNAm-GPT github.com
Foundation model for single-cell whole-genome bisulfite sequencing with whole-genome context modeling at single-CpG resolution.
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sciPENN github.com
RNN-based method for simultaneous protein expression prediction, uncertainty estimation, and cell-type label transfer from CITE-seq and scRNA-seq data.
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JAMIE github.com
Joint variational autoencoder for multimodal single-cell data imputation and embedding.
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Bento github.com
Protein-ligand docking benchmark covering rigid, flexible, de novo, blind, induced-fit, and covalent docking tasks.
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scPair github.com
Bidirectional feedforward network for single-cell multimodal analysis with cross-modality prediction leveraging single-cell atlases.
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DRUML github.com
Ensemble machine learning framework combining standard ML with deep learning to systematically rank anti-cancer drugs from proteomics and RNA-seq data.
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PaccMannRL github.com
Reinforcement learning-based generative model for de novo hit-like anticancer molecule design from transcriptomic data.
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