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Claude Skills by tools-only
github.com/tools-only19,166 skills18 installs6,168 views
- 572 Usage Guide 3bfac6f2ggplot2 is a declarative visualization system based on the Grammar of Graphics. Build publication-quality figures layer by layer.Votes: 0GitHub stars: 9
- 572 Usage Guide 3ebb7620Assesses the genetic health of populations for conservation management. Covers F-statistics and genetic diversity metrics (hierfstat), allelic richness, pairwise population differentiation, runs of homozygosity for inbreeding detection (detectRUNS), and effective population size estimation across multiple time scales: contemporary Ne (NeEstimator LD method), recent Ne trajectory over ~200 generations (GONE2), and deep demographic history over thousands of generations (Stairway Plot 2, PSMC). DesVotes: 0GitHub stars: 9
- 572 Usage Guide 423469c6Detects circadian and ultradian rhythms in time-series omics data. Fits cosinor regression models to estimate rhythm parameters (amplitude, phase, MESOR) and applies non-parametric tests (JTK_CYCLE, RAIN) to identify genes with significant periodic expression at a specified period. Supports both Python (CosinorPy) and R (MetaCycle, RAIN, DiscoRhythm) workflows.Votes: 0GitHub stars: 9
- 572 Usage Guide 4ce205beThis skill covers visualizing Hi-C contact matrices, TADs, loops, and other genomic features using matplotlib, cooltools, and HiCExplorer.Votes: 0GitHub stars: 9
- 572 Usage Guide 50c05801Population structure analysis identifies genetic ancestry and stratification using PCA (continuous clustering) and ADMIXTURE (discrete ancestry proportions). Essential for GWAS stratification control and ancestry inference.Votes: 0GitHub stars: 9
- 572 Usage Guide 58d0a48cIdentify genes with significant temporal expression patterns across time-course experiments using spline models, polynomial regression, or likelihood ratio tests.Votes: 0GitHub stars: 9
- 572 Usage Guide 5a4a9b50Build weighted gene co-expression networks to identify modules of co-regulated genes and relate them to phenotypes. WGCNA constructs a scale-free network from expression data, groups genes into modules based on co-expression patterns, and correlates module eigengenes with sample traits to find biologically relevant modules and hub genes.Votes: 0GitHub stars: 9
- 572 Usage Guide 5a9ba4b3This skill covers modifying protein structures: transforming coordinates, removing/adding atoms and residues, modifying B-factors and occupancies, and building structures programmatically.Votes: 0GitHub stars: 9
- 572 Usage Guide 5deb5784Complete alternative splicing analysis workflow from raw RNA-seq FASTQ files to differential splicing results and visualizations. Includes QC checkpoints and best practices.Votes: 0GitHub stars: 9
- 572 Usage Guide 5ed33940This skill enables AI agents to create static, interactive, and publication-quality visualizations of biological networks. Supports protein interaction networks, gene regulatory networks, co-expression modules, and pathway graphs using NetworkX, PyVis, and Cytoscape automation.Votes: 0GitHub stars: 9
- 572 Usage Guide 60b92d1cThis guide covers generating variant statistics and quality metrics.Votes: 0GitHub stars: 9
- 572 Usage Guide 688798dfThis skill covers quality control, filtering, and normalization for single-cell RNA-seq data using both Seurat (R) and Scanpy (Python). These are essential steps before clustering and downstream analysis.Votes: 0GitHub stars: 9
- 572 Usage Guide 6a16a73fBuild and use spectral libraries containing reference MS2 spectra for faster and more sensitive peptide identification in DIA and targeted proteomics.Votes: 0GitHub stars: 9
- 572 Usage Guide 6f5505a5Extract nucleosome positions from ATAC-seq fragment size patterns using ATACseqQC or NucleoATAC to understand chromatin structure at promoters and regulatory regions.Votes: 0GitHub stars: 9
- 572 Usage Guide 74037a89Build weighted gene co-expression networks to identify modules of co-regulated genes and relate them to phenotypes. WGCNA constructs a scale-free network from expression data, groups genes into modules based on co-expression patterns, and correlates module eigengenes with sample traits to find biologically relevant modules and hub genes.Votes: 0GitHub stars: 9
- 572 Usage Guide 783f4420Estimate circulating tumor DNA fraction from shallow whole-genome sequencing using ichorCNA. Detects copy number alterations and calculates ctDNA percentage for treatment monitoring.Votes: 0GitHub stars: 9
- 572 Usage Guide 7afe2e18WikiPathways is an open, collaborative platform for biological pathways with CC0 license, community curation, and support for 30+ species including many not covered by KEGG or Reactome.Votes: 0GitHub stars: 9
- 572 Usage Guide 7b73ae7aValidate alignment quality with insert size distribution, proper pairing rates, GC bias, strand balance, and other post-alignment metrics before downstream analysis.Votes: 0GitHub stars: 9
- 572 Usage Guide 7b860f68Identify super-enhancers from H3K27ac ChIP-seq data using ROSE or HOMER. Super-enhancers are large clusters of enhancers that control cell identity genes and are often altered in cancer.Votes: 0GitHub stars: 9
- 572 Usage Guide 7f85dfbaThis workflow identifies tumor-specific neoantigens from somatic mutations for personalized cancer vaccine design. It integrates HLA typing, MHC binding prediction, and multi-factor immunogenicity scoring to rank vaccine candidates.Votes: 0GitHub stars: 9
- 572 Usage Guide 82645619Diversity analysis characterizes microbial community structure through alpha (within-sample) and beta (between-sample) diversity metrics using phyloseq and vegan.Votes: 0GitHub stars: 9
- 572 Usage Guide 861951deThis skill covers creating publication-quality visualizations for differential expression results, including MA plots, volcano plots, PCA plots, and heatmaps. Works with both DESeq2 and edgeR output.Votes: 0GitHub stars: 9
- 572 Usage Guide 8de7bfb9Unsupervised clustering identifies cell populations without predefined gates. Useful for discovery and high-dimensional CyTOF/spectral flow data.Votes: 0GitHub stars: 9
- 572 Usage Guide 8e3e3eacThe enrichplot package provides visualization functions for clusterProfiler results, including dot plots, bar plots, networks, and GSEA-specific plots.Votes: 0GitHub stars: 9
- 572 Usage Guide 8ea4f78dDifferential abundance testing identifies taxa that differ significantly between experimental groups while accounting for the compositional nature of microbiome data.Votes: 0GitHub stars: 9
- 572 Usage Guide 8edb9336Delimits putative species boundaries from molecular data using complementary approaches: distance-based partitioning (ASAP), tree-based branching rate models (bPTP, GMYC), and full coalescent analysis (BPP). Follows integrative taxonomy best practice by comparing results across multiple methods to identify consensus species. Designed for DNA barcoding datasets (COI, 12S, ITS, matK), cryptic species complexes, and taxonomic validation studies.Votes: 0GitHub stars: 9
- 572 Usage Guide 93678c76Statistical analysis identifies metabolites associated with biological conditions. Methods range from simple univariate tests to multivariate models for biomarker discovery.Votes: 0GitHub stars: 9
- 572 Usage Guide 963caa6bExplain machine learning predictions on omics data using SHAP values for global and local feature attribution, and LIME for model-agnostic explanations.Votes: 0GitHub stars: 9
- 572 Usage Guide 9c01221aR Markdown combines code, results, and narrative into reproducible documents. Output to HTML, PDF, Word, or presentations.Votes: 0GitHub stars: 9
- 572 Usage Guide 9ed96588Cell-cell communication analysis identifies ligand-receptor interactions between cell types from scRNA-seq data to understand tissue organization, signaling networks, and intercellular coordination.Votes: 0GitHub stars: 9
- 572 Usage Guide A2b6f959This workflow integrates multiple molecular data types (transcriptomics, proteomics, metabolomics, etc.) to discover shared biological signals and cross-modal biomarkers.Votes: 0GitHub stars: 9
- 572 Usage Guide A312aea6Quality control of imputed data is essential before downstream analysis, as poor quality imputation can introduce false positives in GWAS and bias effect estimates.Votes: 0GitHub stars: 9
- 572 Usage Guide A8430ae6Read, write, and convert molecular file formats including SMILES, SDF, MOL2, and PDB. Includes structure standardization pipeline for consistent molecular representations.Votes: 0GitHub stars: 9
- 572 Usage Guide A933bee7This skill covers analyzing cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy. Identify which cell types are communicating and through which signaling pathways.Votes: 0GitHub stars: 9
- 572 Usage Guide Ac8e50fcCreate heatmaps, profile plots, and genome browser-style visualizations for ChIP-seq data using deepTools (CLI), ChIPseeker (R), and Gviz (R).Votes: 0GitHub stars: 9
- 572 Usage Guide B24771b6This skill enables AI agents to help you convert between DNA, RNA, and protein sequences using Biopython. It covers the central dogma operations: transcription, back-transcription, and translation with support for alternative codon tables.Votes: 0GitHub stars: 9
- 572 Usage Guide B3403d15Population structure analysis identifies genetic ancestry and stratification using PCA (continuous clustering) and ADMIXTURE (discrete ancestry proportions). Essential for GWAS stratification control and ancestry inference.Votes: 0GitHub stars: 9
- 572 Usage Guide B6c0a8e7Download and analyze AI-predicted protein structures from the AlphaFold database, including confidence scores (pLDDT) and predicted aligned error (PAE) for assessing prediction quality.Votes: 0GitHub stars: 9
- 572 Usage Guide Be8e727eSelect informative features for biomarker discovery using Boruta all-relevant selection, mRMR minimum redundancy, and LASSO regularization.Votes: 0GitHub stars: 9
- 572 Usage Guide C829575aThis skill enables AI agents to help you run BLAST searches against NCBI databases using Biopython, finding similar sequences to identify unknown genes or find homologs.Votes: 0GitHub stars: 9
- 572 Usage Guide C9449acbmixOmics provides multivariate methods for multi-omics integration, including both supervised (DIABLO, sPLS-DA) and unsupervised (sPLS, sPCA) approaches with sparse feature selection.Votes: 0GitHub stars: 9
- 572 Usage Guide Ca240a8dThis workflow processes raw mass spectrometry data through peak detection, alignment, normalization, statistical analysis, and pathway interpretation.Votes: 0GitHub stars: 9
- 572 Usage Guide D2b88970This skill covers quality control, filtering, normalization, and feature selection for spatial transcriptomics data using Squidpy and Scanpy.Votes: 0GitHub stars: 9
- 572 Usage Guide D4164720Load gene expression count matrices from various quantification tools (featureCounts, Salmon, kallisto, STAR, HTSeq, 10X) into pandas DataFrames for downstream analysis.Votes: 0GitHub stars: 9
- 572 Usage Guide D71e206fThis skill creates publication-quality phylogenetic tree figures using Bio.Phylo's matplotlib integration. It supports customizing labels, colors, and exporting to various image formats.Votes: 0GitHub stars: 9
- 572 Usage Guide D7260645Effective CNV visualization helps identify patterns, validate calls, and communicate findings. This guide covers genome-wide profiles, region-specific plots, and cohort-level comparisons.Votes: 0GitHub stars: 9
- 572 Usage Guide Dda538a3Identify bacterial strain types using MLST, cgMLST, and SNP-based approaches for outbreak investigation and surveillance.Votes: 0GitHub stars: 9
- 572 Usage Guide E926e31aAnalyze cfDNA fragment size distributions and fragmentomics patterns for cancer detection. Extract nucleosome positioning signals and DELFI-style fragmentation profiles.Votes: 0GitHub stars: 9
- 572 Usage Guide F1960aadAnalyze cfDNA methylation patterns for cancer detection and tissue-of-origin analysis. Uses bisulfite sequencing or cfMeDIP-seq for methylation profiling.Votes: 0GitHub stars: 9
- 572 Usage Guide F2597de7ReactomePA provides pathway enrichment analysis using the Reactome database, a curated peer-reviewed knowledgebase of biological pathways with deep hierarchy and reaction-level detail.Votes: 0GitHub stars: 9