cellxgene-census
Queries the CZ CELLxGENE Census programmatically for versioned public single-cell and spatial transcriptomics data. Use when you need population-scale cell…
Skills
Find an Agent Skill for your task. Read the guide and copy the install command.
Updated 11-05 00:16
Data & analytics
17,422 results
citation-management
Comprehensive citation management for academic research. Search OpenAlex, PubMed, and Google Scholar for papers, extract accurate metadata, validate citations,…
cobrapy
Performs constraint-based metabolic modeling with COBRApy, including FBA, pFBA, FVA, gene knockouts, flux sampling, growth media, production envelopes, gap…
database-lookup
Queries documented public database APIs with explicit endpoints, filters, pagination, and provenance. Used when a scientific, regulatory, financial, or other…
datamol
Pythonic wrapper around RDKit with simplified interface and sensible defaults. Preferred for standard drug discovery including SMILES parsing, standardization,…
deeptools
NGS analysis toolkit. BAM to bigWig conversion, QC (correlation, PCA, fingerprints), heatmaps/profiles (TSS, peaks), for ChIP-seq, RNA-seq, ATAC-seq…
depmap
Retrieves and analyzes Cancer Dependency Map (DepMap) release data, including CRISPR Chronos gene effects, cancer model annotations, omics biomarkers, and…
exploratory-data-analysis
Performs bounded, local exploratory analysis of explicitly supported scientific files. Supports redacted CSV/TSV/JSON profiles; optional NumPy, HDF5,…
flowio
Reads, inspects, and writes Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS metadata and channel inspection, NumPy…
geomaster
Supports geospatial research workflows for remote sensing, vector and raster GIS, spatial statistics, terrain and network analysis, and machine learning for…
geopandas
Guidance and local audit tools for Python workflows that directly use GeoPandas GeoSeries, GeoDataFrame, spatial operations, or vector-data I/O.
hugging-science
Discovers and evaluates scientific datasets, models, methodology posts, and Spaces through the Hugging Science catalog. Used when selecting scientific ML…
imaging-data-commons
Queries and downloads public cancer imaging data from NCI Imaging Data Commons. Supports IDC collection discovery, DICOM access, radiology (CT, MR, PET) and…
lamindb
Manages biological datasets and models with LaminDB, including artifact registration, lineage tracking, schema validation, Bionty ontology annotation,…
matchms
Processes, cleans, compares, and searches tandem mass spectra with matchms. Use for MS/MS file I/O, metadata harmonization, peak filtering, spectral…
matlab
Builds, reviews, migrates, and plans MATLAB or GNU Octave numerical workflows. Use for arrays, tabular/time data, tests, projects, graphics, MAT files, and…
neuropixels-analysis
Analyzes Neuropixels extracellular recordings end-to-end with SpikeInterface. Covers loading SpikeGLX/Open Ephys/NWB data, preprocessing, drift/motion…
omero-integration
Inspects and automates microscopy data workflows against OMERO.server with omero-py, BlitzGateway, OMERO CLI, tables, annotations, ROIs, rendering, and…
pacsomatic
Prepares and launches nf-core/pacsomatic matched tumor-normal PacBio HiFi genomics workflows from unaligned BAM inputs. Supports samplesheet generation, pinned…
parallel-web
Uses Parallel CLI for web search, URL extraction, deep research, structured data enrichment, entity discovery, and recurring web monitoring. Best for requests…
pathway-enrichment
Performs pathway and gene-set enrichment analysis on gene lists or ranked gene data and interprets the results. Used when the user has a set of genes…
pydeseq2
Performs bulk RNA-seq differential expression analysis with PyDESeq2, including count validation, formula designs, explicit contrasts, Wald tests, FDR…
pydicom
Reads, inspects, writes, transforms, and preflights local DICOM datasets and pixel data. Applies to DICOM metadata, transfer syntaxes, compression plugins,…
pyhealth
Builds and validates PyHealth clinical machine-learning pipelines for EHR, signals, imaging, and medical codes. Use for PyHealth dataset loading, MIMIC-III/IV,…