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SkillsMP a collecté 579 skills depuis swaruplab/operon. Ouvrez un skill pour examiner sa source et ses détails.
swaruplab/operonAffichage de 40 skills collectés sur 579.
Process and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells/nuclei, and compute morphological features from H&E or IF images. Use when processing tissue images for spatial transcriptomics.
Langue du texte source : anglais
Analyze cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy. Infer intercellular signaling, identify communication pathways, and visualize interaction networks. Use when analyzing cell-cell communication in…
Langue du texte source : anglais
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData. Read Space Ranger outputs, convert formats, and access spatial coordinates. Use when loading Visium, Xenium, MERFISH, or other…
Langue du texte source : anglais
Estimate cell type composition in spatial transcriptomics spots using reference-based deconvolution. Use cell2location, RCTD, SPOTlight, or Tangram to infer cell type proportions from scRNA-seq references. Use when estimating cell type composition in spatial…
Langue du texte source : anglais
Identify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy. Cluster spots considering both expression and spatial context to define anatomical regions. Use when identifying tissue domains or spatial regions.
Langue du texte source : anglais
Analyze high-resolution spatial platforms like Slide-seq, Stereo-seq, and Visium HD. Use when working with subcellular resolution or high-density spatial data.
Langue du texte source : anglais
Build spatial neighbor graphs for spatial transcriptomics data using Squidpy. Compute k-nearest neighbors, Delaunay triangulation, and radius-based connectivity for downstream spatial analyses. Use when building spatial neighborhood graphs.
Langue du texte source : anglais
Quality control, filtering, normalization, and feature selection for spatial transcriptomics data. Calculate QC metrics, filter spots/cells, normalize counts, and identify highly variable genes. Use when filtering and normalizing spatial transcriptomics data.
Langue du texte source : anglais
Analyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization. Use when working with multiplexed imaging data, analyzing protein spatial patterns, or integrating spatial proteomics with…
Langue du texte source : anglais
Compute spatial statistics for spatial transcriptomics data using Squidpy. Calculate Moran's I, Geary's C, spatial autocorrelation, co-occurrence analysis, and neighborhood enrichment. Use when computing spatial autocorrelation or co-occurrence statistics.
Langue du texte source : anglais
Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and annotations overlaid on histology images. Use when visualizing spatial expression patterns.
Langue du texte source : anglais
Automated analysis pipeline for Spatial Transcriptomics (Visium, Xenium) integrating histology and gene expression.
Langue du texte source : anglais
Spatial analyst
Langue du texte source : anglais
Spatial transcriptomics analysis pipeline using squidpy + scanpy. Handles Visium, Xenium, CosMx, MERFISH, Slide-seq, and GeoMx data. Covers loading, quantile-based QC, normalization, clustering, spatial neighborhood analysis (enrichment, co-occurrence,…
Langue du texte source : anglais
AI-powered analysis of T-cell exhaustion states, epigenetic scarring, stem-like T-cell populations, and checkpoint blockade response prediction in cancer immunotherapy.
Langue du texte source : anglais
AI-powered TCR-peptide-MHC interaction prediction using AlphaFold3 and deep learning for therapeutic TCR discovery, neoantigen validation, and T cell immunogenicity assessment.
Langue du texte source : anglais
AI-powered T-cell receptor repertoire analysis for cancer diagnosis, immunotherapy response prediction, and therapeutic TCR selection using deep learning and multi-layer ML approaches.
Langue du texte source : anglais
Comprehensive AI-powered tumor microenvironment immune profiling integrating bulk deconvolution, single-cell analysis, and spatial transcriptomics for immunotherapy biomarker discovery.
Langue du texte source : anglais
Discover novel small molecule binders for protein targets using structure-based and ligand-based approaches. Creates actionable reports with candidate compounds, ADMET profiles, and synthesis feasibility. Use when users ask to find small molecules for a…
Langue du texte source : anglais
Retrieves chemical compound information from PubChem and ChEMBL with disambiguation, cross-referencing, and quality assessment. Creates comprehensive compound profiles with identifiers, properties, bioactivity, and drug information. Use when users need…
Langue du texte source : anglais
Generates comprehensive drug research reports with compound disambiguation, evidence grading, and mandatory completeness sections. Covers identity, chemistry, pharmacology, targets, clinical trials, safety, pharmacogenomics, and ADMET properties. Use when…
Langue du texte source : anglais
Identify and prioritize causal variants at GWAS loci using statistical fine-mapping and locus-to-gene predictions. Computes posterior probabilities for causal variants, links variants to genes via L2G predictions, annotates functional consequences, and…
Langue du texte source : anglais
Interpret genetic variants (SNPs) from GWAS studies by aggregating evidence from multiple databases (GWAS Catalog, Open Targets Genetics, ClinVar). Retrieves variant annotations, GWAS trait associations, fine-mapping evidence, locus-to-gene predictions, and…
Langue du texte source : anglais
Rapid pathogen characterization and drug repurposing analysis for infectious disease outbreaks. Identifies pathogen taxonomy, essential proteins, predicts structures, and screens existing drugs via docking. Use when facing novel pathogens, emerging…
Langue du texte source : anglais
Analyze metabolomics data including metabolite identification, quantification, pathway analysis, and metabolic flux. Processes LC-MS, GC-MS, NMR data from targeted and untargeted experiments. Performs normalization, statistical analysis, pathway enrichment,…
Langue du texte source : anglais
Comprehensive metabolomics research skill for identifying metabolites, analyzing studies, and searching metabolomics databases. Integrates HMDB (220k+ metabolites), MetaboLights, Metabolomics Workbench, and PubChem. Use when asked to identify or annotate…
Langue du texte source : anglais
Analyze drug safety signals from FDA adverse event reports, label warnings, and pharmacogenomic data. Calculates disproportionality measures (PRR, ROR), identifies serious adverse events, assesses pharmacogenomic risk variants. Use when asked about drug…
Langue du texte source : anglais
Provide actionable treatment recommendations for cancer patients based on molecular profile. Interprets tumor mutations, identifies FDA-approved therapies, finds resistance mechanisms, matches clinical trials. Use when oncologist asks about treatment options…
Langue du texte source : anglais
Analyze protein-protein interaction networks using STRING, BioGRID, and SASBDB databases. Maps protein identifiers, retrieves interaction networks with confidence scores, performs functional enrichment analysis (GO/KEGG/Reactome), and optionally includes…
Langue du texte source : anglais
Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles. Creates detailed structure reports with experimental metadata, ligand information, and download links.…
Langue du texte source : anglais
Design novel protein therapeutics (binders, enzymes, scaffolds) using AI-guided de novo design. Uses RFdiffusion for backbone generation, ProteinMPNN for sequence design, ESMFold/AlphaFold2 for validation. Use when asked to design protein binders, therapeutic…
Langue du texte source : anglais
Provide differential diagnosis for patients with suspected rare diseases based on phenotype and genetic data. Matches symptoms to HPO terms, identifies candidate diseases from Orphanet/OMIM, prioritizes genes for testing, interprets variants of uncertain…
Langue du texte source : anglais
Retrieves biological sequences (DNA, RNA, protein) from NCBI and ENA with gene disambiguation, accession type handling, and comprehensive sequence profiles. Creates detailed reports with sequence metadata, cross-database references, and download options. Use…
Langue du texte source : anglais
Computational analysis framework for spatial multi-omics data integration. Given spatially variable genes (SVGs), spatial domain annotations, tissue type, and disease context from spatial transcriptomics/proteomics experiments (10x Visium, MERFISH, DBiTplus,…
Langue du texte source : anglais
Analyze spatial transcriptomics data to map gene expression in tissue architecture. Supports 10x Visium, MERFISH, seqFISH, Slide-seq, and imaging-based platforms. Performs spatial clustering, domain identification, cell-cell proximity analysis, spatial gene…
Langue du texte source : anglais
AI-powered ternary complex prediction for targeted protein degradation, modeling POI-degrader-E3 ligase assemblies to optimize PROTAC and molecular glue efficacy.
Langue du texte source : anglais
Parse trial protocols and patient data to produce criterion-level MET/NOT/UNKNOWN determinations with evidence and gaps for clinical trial screening tasks.
Langue du texte source : anglais
Trial shortlist
Langue du texte source : anglais
AI-powered analysis of tumor clonal architecture, subclonal dynamics, and evolutionary trajectories from multi-region sequencing and longitudinal liquid biopsy data.
Langue du texte source : anglais
AI-powered intratumor heterogeneity analysis for clonal architecture reconstruction, subclonal evolution tracking, and therapy resistance prediction using multi-region and longitudinal sequencing.
Langue du texte source : anglais