clinvar-database
Query NCBI ClinVar via E-utilities for variant clinical significance, pathogenicity, disease associations. Search by gene/rsID/condition/review status; returns…
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Updated 10-27 00:15
Data & analytics
17,003 results
ena-database
ENA REST API for sequences, reads, assemblies, and annotations. Portal API search, Browser API retrieval (XML/FASTA/EMBL), file reports for FASTQ/BAM URLs,…
encode-database
ENCODE Portal REST API for regulatory genomics: TF ChIP-seq, ATAC-seq/DNase-seq peaks, histone marks, and RNA-seq across 1000+ cell types. Search experiments…
gnomad-database
gnomAD v4 population variant frequencies via GraphQL API. Allele counts and frequencies stratified by ancestry (AFR, AMR, EAS, NFE, SAS, FIN, ASJ, MID),…
gtars
Rust-backed Python library for fast genomic token arithmetic and BED processing. High-performance BED I/O, interval set ops (intersect, merge, complement,…
jaspar-database
JASPAR 2024 TF binding profiles via REST API and pyJASPAR. Retrieve PFMs/PWMs by TF name, JASPAR ID, species, or structural class. Scan DNA for TFBS; browse by…
mouse-phenome-database
Retrieve mouse phenotype data from the Jackson Laboratory Mouse Phenome Database (MPD) via its REST API. Browse 520+ projects, look up per-project measure…
quickgo-database
Query EBI QuickGO REST API for GO terms and protein annotations. Fetch term metadata by ID, search by keyword, walk ancestor/descendant hierarchies, download…
regulomedb-database
Query RegulomeDB v2 GET REST API to score variants for regulatory function and retrieve overlapping evidence (TF binding, histone marks, DNase peaks,…
remap-database
Query ReMap 2022 TF ChIP-seq peak database via REST API and BED downloads. Retrieve TF peaks overlapping a region (chr:start-end), peaks near a gene, TFs by…
data-quality-checker
Validate data quality checker operations. Auto-activating skill for Data Pipelines. Triggers on: data quality checker, data quality checker Part of the Data…
schema-validator
Validate schema validator operations. Auto-activating skill for Data Pipelines. Triggers on: schema validator, schema validator Part of the Data Pipelines…
aeon
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection,…
bioservices
Unified Python interface to 40+ bioinformatics services. Use when querying multiple databases (UniProt, KEGG, ChEMBL, Reactome) in a single workflow with…
cellxgene-census
Query the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell…
dask
Distributed computing for larger-than-RAM pandas/NumPy workflows. Use when you need to scale existing pandas/NumPy code beyond memory or across clusters. Best…
datalad
Retrieve, version, and publish scientific datasets with DataLad and git-annex, and capture computational provenance with datalad run, rerun, and…
depmap
Query the Cancer Dependency Map (DepMap) for cancer cell line gene dependency scores (CRISPR Chronos), drug sensitivity data, and gene effect profiles. Use for…
genomic-coordinates
Convert genomic intervals between coordinate conventions, normalise and compare variant representations, and detect assembly or contig-naming mismatches before…
gget
Queries 20+ bioinformatics databases and analysis services through the gget CLI and Python package, covering Ensembl gene search, info and sequences (ref,…
imaging-data-commons
Query and download public cancer imaging data from NCI Imaging Data Commons. Invoke for any question about IDC collections, cancer imaging datasets, DICOM data…
lamindb
Use when working with LaminDB, the open-source lineage-native lakehouse for biological datasets and models. Covers setup, artifact registration, query/search,…
mlflow
Tracks machine learning experiments and manages model lifecycles with MLflow, covering mlflow.log_param, log_metric and log_artifact, autologging for…
networkx
Create, analyze, and visualize complex networks and graphs in Python with NetworkX. Use when working with network/graph data structures, computing graph…