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Data analysis, BI, visualization, datasets, statistics, and ML workflows
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Showing 11,209–11,232 of 12,629 skills
- Tcga PreprocessingGuide Claude through ingesting TCGA sample sheets, expression archives, and clinical carts into omicverse, initialising survival metadata, and exporting annotated AnnData files.Votes: 0GitHub stars: 2,984
- Bio Machine Learning Prediction Explanation--> --- name: bio-machine-learning-prediction-explanation description: Explains machine learning predictions on omics data using SHAP values and LIME for feature attribution. Identifies which genes or features drive classifier decisions. Use when interpreting biomarker classifiers or understanding model predictions. tool_type: python primary_tool: shap measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 2,984
- Bio Machine Learning Omics Classifiers--> --- name: bio-machine-learning-omics-classifiers description: Builds classification models for omics data using RandomForest, XGBoost, and logistic regression with sklearn-compatible APIs. Includes proper preprocessing and evaluation metrics for biomarker classifiers. Use when building diagnostic or prognostic classifiers from expression or variant data. tool_type: python primary_tool: sklearn measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. all...Votes: 0GitHub stars: 2,984
- Bio Machine Learning Model Validation--> --- name: bio-machine-learning-model-validation description: Implements nested cross-validation and stratified splits for unbiased model evaluation on biomedical datasets. Prevents data leakage and overfitting in biomarker discovery. Use when validating classifiers or optimizing hyperparameters on omics data. tool_type: python primary_tool: sklearn measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 2,984
- Bio Machine Learning Biomarker Discovery--> --- name: bio-machine-learning-biomarker-discovery description: Selects informative features for biomarker discovery using Boruta all-relevant selection, mRMR minimum redundancy, and LASSO regularization. Use when identifying biomarkers from high-dimensional omics data. tool_type: python primary_tool: boruta measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 2,984
- Bio Imaging Mass Cytometry PhenotypingCell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification approaches. Use when assigning cell types to segmented IMC cells based on protein marker expression or when phenotyping cells in multiplexed imaging data.Votes: 0GitHub stars: 2,984
- Bio Hi C Analysis Tad DetectionCall topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and hierarchical domain structure. Use when calling TADs from Hi-C insulation scores.Votes: 0GitHub stars: 2,984
- Bio Hi C Analysis Loop CallingDetect 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.Votes: 0GitHub stars: 2,984
- Bio Genome Intervals Interval Arithmetic--> --- name: bio-genome-intervals-interval-arithmetic description: Core interval arithmetic operations including intersect, subtract, merge, complement, map, and groupby using bedtools and pybedtools. Use when finding overlapping regions, removing overlaps, combining adjacent intervals, or transferring annotations between interval files. tool_type: mixed primary_tool: bedtools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_f...Votes: 0GitHub stars: 2,984
- Bio Genome Intervals Coverage Analysis--> --- name: bio-genome-intervals-coverage-analysis description: Calculate read depth and coverage across genomic intervals using bedtools genomecov and coverage. Generate bedGraph files, compute per-base depth, and summarize coverage statistics. Use when assessing sequencing depth, creating coverage tracks, or evaluating target capture efficiency. tool_type: mixed primary_tool: bedtools measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tool...Votes: 0GitHub stars: 2,984
- Bio Genome Intervals Bigwig Tracks--> --- name: bio-genome-intervals-bigwig-tracks description: Create and read bigWig browser tracks for visualizing continuous genomic data. Convert bedGraph to bigWig, extract signal values, and generate coverage tracks using UCSC tools and pyBigWig. Use when preparing coverage tracks for genome browsers or extracting signal at specific regions. tool_type: mixed primary_tool: pyBigWig measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: ...Votes: 0GitHub stars: 2,984
- Bio Genome Assembly Assembly Qc--> --- name: bio-genome-assembly-assembly-qc description: Assess genome assembly quality using QUAST for contiguity metrics and BUSCO for completeness. Essential for evaluating assembly success and comparing assemblers. Use when evaluating assembly completeness and quality. tool_type: cli primary_tool: QUAST measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command --- Evaluate genome assembly quality with cont...Votes: 0GitHub stars: 2,984
- Bio Flow Cytometry Gating AnalysisManual and automated gating for defining cell populations in flow cytometry. Covers rectangular, polygon, and data-driven gates. Use when identifying cell populations through hierarchical gating strategies.Votes: 0GitHub stars: 2,984
- Bio Flow Cytometry Differential AnalysisDifferential abundance and state analysis for cytometry data. Compare cell populations between conditions using statistical methods. Use when testing for significant changes in cell frequencies or marker expression between groups.Votes: 0GitHub stars: 2,984
- Bio Flow Cytometry Compensation TransformationSpillover 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.Votes: 0GitHub stars: 2,984
- Bio Flow Cytometry Clustering PhenotypingUnsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows. Use when discovering cell populations in high-dimensional cytometry data without predefined gates.Votes: 0GitHub stars: 2,984
- Bio Flow Cytometry Bead NormalizationBead-based normalization for CyTOF and high-parameter flow cytometry. Covers EQ bead normalization, signal drift correction, and batch normalization. Use when correcting instrument drift in CyTOF or harmonizing data across batches.Votes: 0GitHub stars: 2,984
- Bio Expression Matrix Metadata Joins--> --- name: bio-expression-matrix-metadata-joins description: Merge sample metadata with count matrices and add gene annotations. Use when preparing data for differential expression analysis or visualization. tool_type: mixed primary_tool: pandas measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 2,984
- Bio Experimental Design Sample Size--> --- name: bio-experimental-design-sample-size description: Estimates required sample sizes for differential expression, ChIP-seq, methylation, and proteomics studies. Use when budgeting experiments, writing grant proposals, or determining minimum replicates needed to achieve statistical significance for expected effect sizes. tool_type: r primary_tool: ssizeRNA measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_she...Votes: 0GitHub stars: 2,984
- Bio Epitranscriptomics M6a Differential--> --- name: bio-epitranscriptomics-m6a-differential description: Identify differential m6A methylation between conditions from MeRIP-seq. Use when comparing epitranscriptomic changes between treatment groups or cell states. tool_type: r primary_tool: exomePeak2 measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 2,984
- Bio De ResultsExtract, filter, annotate, and export differential expression results from DESeq2 or edgeR. Use for identifying significant genes, applying multiple testing corrections, adding gene annotations, and preparing results for downstream analysis. Use when filtering and exporting DE analysis results.Votes: 0GitHub stars: 2,984
- Bio De Edger BasicsPerform differential expression analysis using edgeR in R/Bioconductor. Use for analyzing RNA-seq count data with the quasi-likelihood F-test framework, creating DGEList objects, normalization, dispersion estimation, and statistical testing. Use when performing DE analysis with edgeR.Votes: 0GitHub stars: 2,984
- Bio De Deseq2 BasicsPerform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creating DESeqDataSet objects, running the DESeq workflow, and extracting results with log fold change shrinkage. Use when performing DE analysis with DESeq2.Votes: 0GitHub stars: 2,984
- Bio Data Visualization Upset Plots--> --- name: bio-data-visualization-upset-plots description: Create UpSet plots to visualize set intersections as an alternative to Venn diagrams using UpSetR or upsetplot. Use when comparing overlapping gene sets, peak sets, or sample groups with more than 3 sets. tool_type: mixed primary_tool: UpSetR measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes. allowed-tools: - read_file - run_shell_command ---Votes: 0GitHub stars: 2,984