Computational Biology
371 items from inoue0426/awesome-computational-biology ★159
-
PrePR-CT github.com
Graph-based model using cell-type-specific co-expression networks as inductive priors for small-data chemical perturbation response prediction.
-
PASO github.com
Pathway-aware multi-omics drug response model combining pathway-difference features, multi-scale convolutions, Transformer encoding, and drug SMILES.
-
Broad Institute Single Cell Portal singlecell.broadinstitute.org
Reducing barriers and accelerating single-cell research.
-
UCSC Genome Browser genome.ucsc.edu
Interactively visualize genomic data.
-
Ensembl ensembl.org
A genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation.
-
EBI Single Cell Expression Atlas ebi.ac.uk
Single cell gene expression across species.
-
cBioPortal for Cancer Genomics cbioportal.org
Visualization, analysis and download of large-scale cancer genomics data sets.
-
OpenMM openmm.org
High-performance toolkit for molecular simulation and GPU-accelerated MD.
-
Gromacs gromacs.org
Molecular dynamics simulation package for biochemical molecules.
-
GenBank ncbi.nlm.nih.gov
NCBI's database of genetic sequences.
-
UK Biobank ukbiobank.ac.uk
A large-scale biomedical database and research resource with 500,000 research participants.
-
Comparative Toxicogenomics Database ctdbase.org
paper - A database of manually curated associations between chemicals, gene products, phenotypes, diseases, and environmental exposures. Useful for assembling ontologies of the related concepts, such as types of chemicals.
-
Biopython biopython.org
paper - code - Python tools primarily intended for bioinformatics and computational molecular biology purposes, but also a convenient way to obtain data, including documents/abstracts from PubMed (see Chapter 9 of the documentation).
-
OmicsFM github.com
Modality-agnostic molecular-expression foundation model with matched proteomics, bulk-transcriptomics, and single-cell-transcriptomics checkpoints.
-
ChromFound github.com
Genome-aware scATAC-seq foundation model pretrained on 1.97M cells across tissues and disease contexts for zero-shot cell representations, annotation, and cross-omics prediction.
-
TESSERA github.com
Cancer-genome foundation model jointly pretrained on somatic SNVs and copy-number alterations from TCGA using masked reconstruction and cross-modal contrastive learning.
-
cycleCDR github.com
Interpretable cycle-consistency framework for modeling cellular responses to drug perturbations.
-
DeepAEG github.com
GNN embedding + attention mechanism.
-
MCPINN github.com
Drug discovery via compound-protein interaction and machine learning.
-
NbBayesLM github.com
Bayesian neural network integrating protein language model embeddings and physicochemical features to predict nanobody thermostability with uncertainty estimates. Paper
-
Chem-PerturBridge github.com
Harmonized compendium and processing pipelines for small-molecule perturbation transcriptomics across heterogeneous assays and gene panels.
-
drGAT github.com
Attention-based model for drug response prediction with gene explainability.
-
THERAPI github.com
Cell-line-to-patient transfer framework that aligns tumor transcriptomes with cancer cell lines and integrates perturbation and gene-level representations for patient drug response prediction.
-
Casanovo Foundation github.com
Tandem mass-spectrometry proteomics foundation model that reuses a pretrained Casanovo spectrum encoder for spectrum quality, chimericity, and post-translational-modification prediction.
-
DGDRP github.com
Multi-view embedding neural network.
-
DrugAgent github.com
Multi-agent biomedical evidence synthesis framework for computational drug discovery with reliability-aware aggregation.
-
ZINC ligand discovery database zinc.docking.org
Free database of commercially-available compounds for virtual screening.
-
WikiPathways wikipathways.org
Database of biological pathways.
-
UniRef uniprot.org
Non-redundant sequence database clustering UniProtKB entries at multiple sequence identity thresholds.
-
UniProt REST API uniprot.org
Programmatic access to protein sequence and functional annotation data.
-
UniProt uniprot.org
Functional information on proteins.
-
Uniclust uniclust.mmseqs.com
Clustered protein sequence databases.
-
Tox21 tripod.nih.gov
12,707 compounds tested in 12 nuclear receptor and stress-response pathway biochemical assays for toxicity prediction.
-
BioGRID thebiogrid.org
Protein, genetic, and chemical interactions.
-
ClinTox tdcommons.ai
Clinical toxicity dataset contrasting FDA-approved drugs with those that failed clinical trials due to toxicity.
-
Therapeutics Data Commons (TDC) tdcommons.ai
Unified benchmark suite covering ADMET, drug-target interaction, drug response, and more.
-
Tabula Sapiens tabula-sapiens-portal.ds.czbiohub.org
Comprehensive human single-cell atlas of ~500K cells from 24 organs and tissues across multiple donors.
-
Tabula Muris tabula-muris.ds.czbiohub.org
Comprehensive single-cell atlas of 20 mouse organs and tissues, enabling cross-tissue and cross-species comparisons.
-
STRING string-db.org
PPI networks for multiple organisms.
-
STITCH stitch.embl.de
Chemical-protein interactions.
-
Davis kinase inhibitors DB staff.cs.utu.fi
Experimental kinase inhibitor binding affinity dataset for protein–ligand interaction research.
-
Squidpy squidpy.readthedocs.io
Python library for spatial single-cell analysis.
-
SNAP snap.stanford.edu
Dataset of drug-gene interactions.
-
Cancer Cell Line Encyclopedia sites.broadinstitute.org
Database of ~1000 cancer cell lines.
-
Frangieh et al. 2021 Perturb-CITE-seq singlecell.broadinstitute.org
Multimodal CRISPR knockout screen with RNA and surface-protein readouts in patient-derived melanoma models under immune-related conditions.
-
SIGNOR 2.0 signor.uniroma2.it
Database of causal signaling interactions and pathways, with signed and directed relationships between proteins.
-
SIDER (Side Effect Resource) sideeffects.embl.de
Database of 1,430 approved drugs with their recorded adverse drug reactions across 27 system-organ classes.
-
SeqBench seqbench.com
Web-based molecular biology sequence workbench for primer design, cloning simulation (Gibson, Golden Gate, restriction digest), CRISPR guide RNA design, and sequence analysis, with a public REST API, OpenAPI 3.1 spec, and MCP server.
-
scvi-tools scvi-tools.org
Probabilistic models for single-cell omics data analysis.
-
Scanpy scanpy.readthedocs.io
Python library for scRNA-seq analysis.
- next page of items loading…
