GitHub
benchling-integration
Benchling R&D platform integration. Access registry (DNA, proteins), inventory, ELN entries, workflows via API, build Benchling Apps, query Data Warehouse, for lab data management automation.
☆ 18,938Voir le skill
Skills IA databases bioinformatics
Découvrez les skills databases bioinformatics, comparez leurs dépôts et consultez leurs instructions.
Catégories: databases bioinformatics
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GitHub
metabolomics-workbench-database
Access NIH Metabolomics Workbench via REST API (4,200+ studies). Query metabolites, RefMet nomenclature, MS/NMR data, m/z searches, study metadata, for metabolomics and biomarker discovery.
☆ 18,938Voir le skill
GitHub
bioservices
Primary Python tool for 40+ bioinformatics services. Preferred for multi-database workflows: UniProt, KEGG, ChEMBL, PubChem, Reactome, QuickGO. Unified API for queries, ID mapping, pathway analysis. For direct...
☆ 18,938Voir le skill
GitHub
lamindb
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spa...
☆ 18,938Voir le skill
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...
☆ 18,938Voir le skill
GitHub
brenda-database
Access BRENDA enzyme database via SOAP API. Retrieve kinetic parameters (Km, kcat), reaction equations, organism data, and substrate-specific enzyme information for biochemical research and metabolic pathway an...
☆ 18,938Voir le skill
GitHub
pyopenms
Python interface to OpenMS for mass spectrometry data analysis. Use for LC-MS/MS proteomics and metabolomics workflows including file handling (mzML, mzXML, mzTab, FASTA, pepXML, protXML, mzIdentML), signal pro...
☆ 18,938Voir le skill
GitHub
scvi-tools
Deep generative models for single-cell omics. Use when you need probabilistic batch correction (scVI), transfer learning, differential expression with uncertainty, or multi-modal integration (TOTALVI, MultiVI)....
☆ 8,603Voir le skill
GitHub
geniml
This skill should be used when working with genomic interval data (BED files) for machine learning tasks. Use for training region embeddings (Region2Vec, BEDspace), single-cell ATAC-seq analysis (scEmbed), buil...
☆ 8,603Voir le skill
GitHub
gene-database
Query NCBI Gene via E-utilities/Datasets API. Search by symbol/ID, retrieve gene info (RefSeqs, GO, locations, phenotypes), batch lookups, for gene annotation and functional analysis.
☆ 8,603Voir le skill
GitHub
lamindb
This skill should be used when working with LaminDB, an open-source data framework for biology that makes data queryable, traceable, reproducible, and FAIR. Use when managing biological datasets (scRNA-seq, spa...
☆ 8,603Voir le skill
GitHub
pysam
Genomic file toolkit. Read/write SAM/BAM/CRAM alignments, VCF/BCF variants, FASTA/FASTQ sequences, extract regions, calculate coverage, for NGS data processing pipelines.
☆ 8,603Voir le skill
GitHub
esm
Comprehensive toolkit for protein language models including ESM3 (generative multimodal protein design across sequence, structure, and function) and ESM C (efficient protein embeddings and representations). Use...
☆ 8,603Voir le skill
GitHub
rdkit
Cheminformatics toolkit for fine-grained molecular control. SMILES/SDF parsing, descriptors (MW, LogP, TPSA), fingerprints, substructure search, 2D/3D generation, similarity, reactions. For standard workflows w...
☆ 8,603Voir le skill
GitHub
adaptyv
Cloud laboratory platform for automated protein testing and validation. Use when designing proteins and needing experimental validation including binding assays, expression testing, thermostability measurements...
☆ 8,603Voir le skill
GitHub
chembl-database
Query ChEMBL bioactive molecules and drug discovery data. Search compounds by structure/properties, retrieve bioactivity data (IC50, Ki), find inhibitors, perform SAR studies, for medicinal chemistry.
☆ 8,603Voir le skill
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.
☆ 8,603Voir le skill
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...
☆ 8,603Voir le 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...
☆ 8,603Voir le skill
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.
☆ 8,603Voir le skill
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...
☆ 8,603Voir le skill
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...
☆ 8,603Voir le skill
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...
☆ 8,603Voir le skill
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.
☆ 8,603Voir le skill
Le classement utilise les étoiles du dépôt GitHub indexé. Plusieurs skills peuvent partager ce nombre : ce n’est ni un nombre d’installations ni une note de qualité.