Topic: skills
17,247 skills in this topic.
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bio-clip-seq-clip-motif-analysis
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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cell-free-expression
Guidance for cell-free protein synthesis (CFPS) optimization. Use when: (1) Planning CFPS experiments, (2) Troubleshooting low yield or aggregation, (3) Optimizing DNA template design for CFPS, (4) Expressing difficult proteins (disulfide-rich, toxic, membrane).
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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bio-causal-genomics-pleiotropy-detection
Detect and correct for horizontal pleiotropy in Mendelian randomization analyses using MR-PRESSO for outlier removal, MR-Egger regression for directional pleiotropy, and Steiger filtering for variant directionality. Use when validating MR results, detecting pleiotropic instruments, or running sensitivity analyses for causal inference.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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bio-workflows-longread-sv-pipeline
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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bio-genome-intervals-interval-arithmetic
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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bio-single-cell-preprocessing
Quality control, filtering, and normalization for single-cell RNA-seq using Seurat (R) and Scanpy (Python). Use for calculating QC metrics, filtering cells and genes, normalizing counts, identifying highly variable genes, and scaling data. Use when filtering, normalizing, and selecting features in single-cell data.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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bio-pathway-kegg-pathways
KEGG pathway and module enrichment analysis using clusterProfiler enrichKEGG and enrichMKEGG. Use when identifying metabolic and signaling pathways over-represented in a gene list. Supports 4000+ organisms via KEGG online database.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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bio-workflows-spatial-pipeline
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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slurm-job-script-generator
Generate SLURM `sbatch` job scripts and sanity-check HPC resource requests (nodes, tasks, CPUs, memory, GPUs) for simulation runs. Use when preparing submission scripts, deciding MPI vs MPI+OpenMP layouts, standardizing `#SBATCH` directives, or debugging job launch configuration (`sbatch`/`srun`).
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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pdf-processing-pro
Production-ready PDF processing with forms, tables, OCR, validation, and batch operations. Use when working with complex PDF workflows in production environments, processing large volumes of PDFs, or requiring robust error handling and validation.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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ontology-explorer
Parse, navigate, and query materials science ontology structure (classes, properties, hierarchy). Use when exploring an ontology like CMSO, understanding class relationships, finding properties for a given class, or searching for ontology terms related to a materials science concept. Supports OWL/XML format from the OCDO ecosystem (CMSO, ASMO, CDCO, PODO, PLDO, LDO).
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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bio-flow-cytometry-compensation-transformation
Spillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application, and biexponential/arcsinh transforms. Use when correcting spectral overlap between fluorophores or transforming data for analysis.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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bio-workflows-chipseq-pipeline
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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bio-cfdna-preprocessing
Preprocesses cell-free DNA sequencing data including adapter trimming, alignment optimized for short fragments, and UMI-aware duplicate removal using fgbio. Applies cfDNA-specific quality thresholds and fragment length filtering. Use when processing plasma cfDNA sequencing data before downstream analysis.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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drugbank-search
Search DrugBank comprehensive drug database with natural language queries. Drug mechanisms, interactions, and safety data powered by Valyu.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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deep-visual-proteomics-agent
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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tooluniverse-spatial-transcriptomics
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 expression patterns, tissue architecture mapping, and integration with single-cell data. Use when analyzing spatial transcriptomics datasets, studying tissue organization, identifying spatial expression patterns, mapping cell-cell interactions in tissue context, characterizing tumor microenvironment spatial structure, or integrating spatial and single-cell RNA-seq data for comprehensive tissue analysis.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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simo-multiomics-integration-agent
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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aeon
This skill should be used for time series machine learning tasks including classification, regression, clustering, forecasting, anomaly detection, segmentation, and similarity search. Use when working with temporal data, sequential patterns, or time-indexed observations requiring specialized algorithms beyond standard ML approaches. Particularly suited for univariate and multivariate time series analysis with scikit-learn compatible APIs.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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pathml
Computational pathology toolkit for analyzing whole-slide images (WSI) and multiparametric imaging data. Use this skill when working with histopathology slides, H&E stained images, multiplex immunofluorescence (CODEX, Vectra), spatial proteomics, nucleus detection/segmentation, tissue graph construction, or training ML models on pathology data. Supports 160+ slide formats including Aperio SVS, NDPI, DICOM, OME-TIFF for digital pathology workflows.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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single-cell-cellphonedb-communication-mapping
Run omicverse's CellPhoneDB v5 wrapper on annotated single-cell data to infer ligand-receptor networks and produce CellChat-style visualisations.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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tooluniverse-epigenomics
Production-ready genomics and epigenomics data processing for BixBench questions. Handles methylation array analysis (CpG filtering, differential methylation, age-related CpG detection, chromosome-level density), ChIP-seq peak analysis (peak calling, motif enrichment, coverage stats), ATAC-seq chromatin accessibility, multi-omics integration (expression + methylation correlation), and genome-wide statistics. Pure Python computation (pandas, scipy, numpy, pysam, statsmodels) plus ToolUniverse annotation tools (Ensembl, ENCODE, SCREEN, JASPAR, ReMap, RegulomeDB, ChIPAtlas). Supports BED, BigWig, methylation beta-value matrices, Illumina manifest files, and multi-sample clinical data. Use when processing methylation data, ChIP-seq peaks, ATAC-seq signals, or answering questions about CpG sites, differential methylation, chromatin accessibility, histone marks, or epigenomic statistics.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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bio-longread-alignment
Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use when aligning ONT or PacBio reads to a reference genome for variant calling, SV detection, or coverage analysis.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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bio-vcf-manipulation
Merge, concatenate, sort, intersect, and subset VCF files using bcftools. Use when combining variant files, comparing call sets, or restructuring VCF data.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009