GitHub
pubchem-database
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
☆ 8,603View skill
documentation scientific computing AI Skills
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GitHub
omero-integration
Microscopy data management platform. Access images via Python, retrieve datasets, analyze pixels, manage ROIs/annotations, batch processing, for high-content screening and microscopy workflows.
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GitHub
scanpy
Standard single-cell RNA-seq analysis pipeline. Use for QC, normalization, dimensionality reduction (PCA/UMAP/t-SNE), clustering, differential expression, and visualization. Best for exploratory scRNA-seq analy...
☆ 8,603View skill
GitHub
rowan
Cloud-based quantum chemistry platform with Python API. Preferred for computational chemistry workflows including pKa prediction, geometry optimization, conformer searching, molecular property calculations, pro...
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GitHub
string-database
Query STRING API for protein-protein interactions (59M proteins, 20B interactions). Network analysis, GO/KEGG enrichment, interaction discovery, 5000+ species, for systems biology.
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GitHub
gget
Fast CLI/Python queries to 20+ bioinformatics databases. Use for quick lookups: gene info, BLAST searches, AlphaFold structures, enrichment analysis. Best for interactive exploration, simple queries. For batch...
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GitHub
biopython
Comprehensive molecular biology toolkit. Use for sequence manipulation, file parsing (FASTA/GenBank/PDB), phylogenetics, and programmatic NCBI/PubMed access (Bio.Entrez). Best for batch processing, custom bioin...
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GitHub
kegg-database
Direct REST API access to KEGG (academic use only). Pathway analysis, gene-pathway mapping, metabolic pathways, drug interactions, ID conversion. For Python workflows with multiple databases, prefer bioservices...
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GitHub
cosmic-database
Access COSMIC cancer mutation database. Query somatic mutations, Cancer Gene Census, mutational signatures, gene fusions, for cancer research and precision oncology. Requires authentication.
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GitHub
clinpgx-database
Access ClinPGx pharmacogenomics data (successor to PharmGKB). Query gene-drug interactions, CPIC guidelines, allele functions, for precision medicine and genotype-guided dosing decisions.
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GitHub
molfeat
Molecular featurization for ML (100+ featurizers). ECFP, MACCS, descriptors, pretrained models (ChemBERTa), convert SMILES to features, for QSAR and molecular ML.
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GitHub
hypogenic
Automated LLM-driven hypothesis generation and testing on tabular datasets. Use when you want to systematically explore hypotheses about patterns in empirical data (e.g., deception detection, content analysis)....
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GitHub
dnanexus-integration
DNAnexus cloud genomics platform. Build apps/applets, manage data (upload/download), dxpy Python SDK, run workflows, FASTQ/BAM/VCF, for genomics pipeline development and execution.
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GitHub
clinical-decision-support
Generate professional clinical decision support (CDS) documents for pharmaceutical and clinical research settings, including patient cohort analyses (biomarker-stratified with outcomes) and treatment recommenda...
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GitHub
bioservices
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with consistent API. Best for cross-database analysis, ID map...
☆ 8,603View skill
GitHub
deepchem
Molecular ML with diverse featurizers and pre-built datasets. Use for property prediction (ADMET, toxicity) with traditional ML or GNNs when you want extensive featurization options and MoleculeNet benchmarks....
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GitHub
research-lookup
Look up current research information using Perplexity Sonar Pro Search or Sonar Reasoning Pro models through OpenRouter. Automatically selects the best model based on query complexity. Search academic papers, r...
☆ 8,603View skill
GitHub
opentargets-database
Query Open Targets Platform for target-disease associations, drug target discovery, tractability/safety data, genetics/omics evidence, known drugs, for therapeutic target identification.
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GitHub
denario
Multiagent AI system for scientific research assistance that automates research workflows from data analysis to publication. This skill should be used when generating research ideas from datasets, developing re...
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GitHub
ena-database
Access European Nucleotide Archive via API/FTP. Retrieve DNA/RNA sequences, raw reads (FASTQ), genome assemblies by accession, for genomics and bioinformatics pipelines. Supports multiple formats.
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GitHub
cellxgene-census
Query the CELLxGENE Census (61M+ cells) programmatically. Use when you need expression data across tissues, diseases, or cell types from the largest curated single-cell atlas. Best for population-scale queries,...
☆ 8,603View skill
GitHub
deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq visualization.
☆ 8,603View skill
GitHub
pyopenms
Complete mass spectrometry analysis platform. Use for proteomics workflows feature detection, peptide identification, protein quantification, and complex LC-MS/MS pipelines. Supports extensive file formats and...
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GitHub
diffdock
Diffusion-based molecular docking. Predict protein-ligand binding poses from PDB/SMILES, confidence scores, virtual screening, for structure-based drug design. Not for affinity prediction.
☆ 8,603View skill
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