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Topic: skills

17,247 skills in this topic.

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
bio-methylation-methylkit DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons. Use when analyzing single-base methylation patterns, comparing samples, or preparing data for DMR detection.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-restriction-fragment-analysis
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-workflows-hic-pipeline
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-workflows-spatial-pipeline
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-causal-genomics-fine-mapping Identify likely causal variants within GWAS loci using SuSiE for sum of single effects regression and FINEMAP for shotgun stochastic search. Computes posterior inclusion probabilities and credible sets to prioritize variants for functional follow-up. Use when narrowing GWAS association signals to candidate causal variants or building credible sets for functional validation.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-workflows-biomarker-pipeline
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-clinical-databases-variant-prioritization Filter and prioritize variants by pathogenicity, population frequency, and clinical evidence for rare disease analysis. Use when identifying candidate disease-causing variants from exome or genome sequencing.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-single-cell-splicing Analyzes alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or leafcutter2 for cluster-based analysis with NMD detection. Identifies cell-type-specific splicing patterns. Use when analyzing isoform usage in scRNA-seq or finding splicing differences between cell populations.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-causal-genomics-mendelian-randomization Estimate causal effects between exposures and outcomes using genetic variants as instrumental variables with TwoSampleMR. Implements IVW, MR-Egger, weighted median, and MR-PRESSO methods for robust causal inference from GWAS summary statistics. Use when testing whether an exposure causally affects an outcome using genetic instruments.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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
bio-genome-engineering-off-target-prediction Predict CRISPR off-target sites using Cas-OFFinder and CFD scoring algorithms. Identify potential unintended cleavage sites genome-wide and assess guide specificity. Use when evaluating guide RNA specificity or selecting guides with minimal off-target risk.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-comparative-genomics-ancestral-reconstruction
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-workflows-metabolomics-pipeline
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-long-read-sequencing-nanopore-methylation Calls DNA methylation from Oxford Nanopore sequencing data using signal-level analysis. Use when detecting 5mC or 6mA modifications directly from nanopore reads without bisulfite conversion.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
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
bio-hi-c-analysis-loop-calling Detect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods. Identify CTCF-mediated loops and enhancer-promoter contacts. Use when detecting chromatin loops from Hi-C data.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-clip-seq-clip-motif-analysis
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-compressed-files Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with .gz or .bz2 sequence files. Use BGZF for indexable compressed files.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bio-microbiome-diversity-analysis Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample dissimilarity with phyloseq and vegan. Use when comparing community composition across samples or testing for group differences in microbiome structure.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
convergence-study Spatial and temporal convergence analysis with Richardson extrapolation and Grid Convergence Index (GCI) for solution verification
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
bulk-rna-seq-differential-expression-with-omicverse Guide Claude through omicverse's bulk RNA-seq DEG pipeline, from gene ID mapping and DESeq2 normalization to statistical testing, visualization, and pathway enrichment. Use when a user has bulk count matrices and needs differential expression analysis in omicverse.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
arboreto Infer gene regulatory networks (GRNs) from gene expression data using scalable algorithms (GRNBoost2, GENIE3). Use when analyzing transcriptomics data (bulk RNA-seq, single-cell RNA-seq) to identify transcription factor-target gene relationships and regulatory interactions. Supports distributed computation for large-scale datasets.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009
alphafold-database Access AlphaFold's 200M+ AI-predicted protein structures. Retrieve structures by UniProt ID, download PDB/mmCIF files, analyze confidence metrics (pLDDT, PAE), for drug discovery and structural biology.
FreedomIntelligence/OpenClaw-Medical-Skills 2,009