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Complete Tier 2 investigation workflow. Orchestrates deep investigation of escalated cases: deep-dive-ioc, correlate-ioc, specialized triage (malware/login), pivot-on-ioc, and generate comprehensive report. Use for escalated cases requiring thorough...
Deploy and configure applications on Vercel. Use when deploying Next.js apps, configuring serverless functions, setting up edge functions, or managing Vercel projects. Triggers on Vercel, deploy, serverless, edge function, Next.js deployment.
Build LLM applications with LangChain and LangGraph. Use when creating RAG pipelines, agent workflows, chains, or complex LLM orchestration. Triggers on LangChain, LangGraph, LCEL, RAG, retrieval, agent chain.
Fetch and display GitHub trending repositories and developers. Use when building dashboards showing trending repos, discovering popular projects, or tracking GitHub trends. Triggers on GitHub trending, trending repos, popular repositories, GitHub dis...
Check and configure code coverage thresholds and reporting
Manage modular rules in .claude/rules/ directory. Supports path-specific rules with glob patterns, brace expansion, and user-level rules.
Query dbSNP for rsID lookups, variant annotations, and cross-references to other databases. Use when mapping between rsIDs and genomic coordinates or retrieving basic variant information.
Read and manipulate Flow Cytometry Standard (FCS) files. Covers loading data, accessing parameters, and basic data exploration. Use when loading and inspecting flow or mass cytometry data before preprocessing.
Analyze BCR repertoires for somatic hypermutation, clonal lineages, and B cell phylogenetics using the Immcantation framework. Use when studying B cell affinity maturation, germinal center dynamics, or antibody evolution.
Fast miRNA quantification with isomiR detection and A-to-I editing analysis using miRge3. Use when quantifying known miRNAs quickly or analyzing isomiR variants and RNA editing.
Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific considerations. Use when identifying miRNAs that change between treatment groups, disease states, or developmental stages.
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.
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.
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.
Call accessible chromatin regions from ATAC-seq data using MACS3 with ATAC-specific parameters. Use when identifying open chromatin regions from aligned ATAC-seq BAM files, different from ChIP-seq peak calling.
Calculates molecular descriptors and fingerprints using RDKit. Computes Morgan fingerprints (ECFP), MACCS keys, Lipinski properties, QED drug-likeness, TPSA, and 3D conformer descriptors. Use when featurizing molecules for machine learning or filteri...
Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format. Use when generating analysis reports with RMarkdown.
MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) for pooled CRISPR screen analysis. Covers count normalization, gene ranking, and pathway analysis. Use when identifying essential genes, drug targets, or resistance mechanisms from dro...
Count reads per gene from aligned BAM files using Subread featureCounts. Use when processing BAM files from STAR/HISAT2 to generate gene-level counts for DESeq2/edgeR.
Select and apply colorblind-friendly palettes for scientific figures using viridis, RColorBrewer, and custom color schemes. Use when selecting colorblind-friendly palettes for figures.
Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, insertions, inversions, translocations, or complex rearrangements from ONT or PacBio data, especially those missed by short-read meth...
Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data with library-free or library-based workflows for deep proteome profiling.
Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta. Use when importing transcript counts into R for DESeq2/edgeR.
Differential 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.
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