Agent skills

Skills for claude-code

Read straight from the source repositories, not from submitted listings. Every skill shows what it does, what is inside, where it came from — and whether attention around its source is actually growing.

Toolclaude-code 29,140codex 4,755cursor 3,111copilot 976windsurf 55cline 34
CategoryWorkflow & Productivity 4,979AI & Agents 3,037Data & Analytics 2,345Code Review & Quality 1,376Backend & API 1,244Security 1,194Design & Presentation 1,154Documentation 965Content & Marketing 916Testing & QA 777DevOps & Cloud 576Databases 550Frontend 469Business & Finance 328Media & Video 257Other 9,833
62,644 found
2,4012,448 · page 51 / 1,306
bio-microbiome-qiime2-workflowQIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance…FreedomIntelligencescriptsbio-molecular-descriptorsCalculates molecular descriptors and fingerprints using RDKit. Computes Morgan fingerprints (ECFP), MACCS keys, Lipinski…FreedomIntelligencescriptsbio-molecular-ioReads, writes, and converts molecular file formats (SMILES, SDF, MOL2, PDB) using RDKit and Open Babel. Handles structure…FreedomIntelligencescriptsbio-paired-end-fastqHandle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs…FreedomIntelligencescriptsbio-proteomics-data-importLoad and parse mass spectrometry data formats including mzML, mzXML, and quantification tool outputs like MaxQuant…FreedomIntelligencescriptsbio-proteomics-dia-analysisData-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Use when analyzing DIA mass spectrometry data…FreedomIntelligencescriptsbio-proteomics-peptide-identificationPeptide-spectrum matching and protein identification from MS/MS data. Use when identifying peptides from tandem mass spectra.…FreedomIntelligencescriptsbio-proteomics-protein-inferenceProtein grouping and inference from peptide identifications. Use when resolving protein ambiguity from shared peptides. Handles…FreedomIntelligencescriptsbio-proteomics-proteomics-qcQuality control and assessment for proteomics data. Use when evaluating proteomics data quality before downstream analysis.…FreedomIntelligencescriptsbio-proteomics-ptm-analysisPost-translational modification analysis including phosphorylation, acetylation, and ubiquitination. Covers site localization…FreedomIntelligencescriptsbio-proteomics-quantificationProtein quantification from mass spectrometry data including label-free (LFQ, intensity-based), isobaric labeling (TMT, iTRAQ)…FreedomIntelligencescriptsbio-proteomics-spectral-librariesBuild, manage, and search spectral libraries for proteomics. Use when creating or working with spectral libraries for DIA…FreedomIntelligencescriptsbio-reaction-enumerationEnumerates chemical libraries through reaction SMARTS transformations using RDKit. Generates virtual compound libraries from…FreedomIntelligencescriptsbio-read-qc-adapter-trimmingRemove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Illumina…FreedomIntelligencescriptsbio-read-qc-contamination-screeningDetect sample contamination and cross-species reads using FastQ Screen. Screen reads against multiple reference genomes to…FreedomIntelligencescriptsbio-read-qc-fastp-workflowAll-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML…FreedomIntelligencescriptsbio-read-qc-quality-filteringFilter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove…FreedomIntelligencescriptsbio-read-qc-quality-reportsGenerate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter content, GC…FreedomIntelligencescriptsbio-read-qc-umi-processingExtract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep includes…FreedomIntelligencescriptsbio-ribo-seq-orf-detectionDetect and quantify translated ORFs from Ribo-seq data including uORFs and novel ORFs using RiboCode and ORFquant. Use when…FreedomIntelligencescriptsbio-ribo-seq-riboseq-preprocessingPreprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when preparing…FreedomIntelligencescriptsbio-ribo-seq-ribosome-periodicityValidate Ribo-seq data quality by checking 3-nucleotide periodicity and calculating P-site offsets. Use when assessing library…FreedomIntelligencescriptsbio-ribo-seq-ribosome-stallingDetect ribosome pausing and stalling sites from Ribo-seq data at codon resolution. Use when studying translational regulation…FreedomIntelligencescriptsbio-ribo-seq-translation-efficiencyCalculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA abundance. Use when comparing translational…FreedomIntelligencescriptsbio-sashimi-plotsCreates sashimi plots showing RNA-seq read coverage and splice junction counts using ggsashimi or rmats2sashimiplot. Visualizes…FreedomIntelligencescriptsbio-sequence-statisticsCalculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing…FreedomIntelligencescriptsbio-similarity-searchingPerforms molecular similarity searches using Tanimoto coefficient on fingerprints via RDKit. Finds structurally similar compounds…FreedomIntelligencescriptsbio-single-cell-metabolite-communicationAnalyze metabolite-mediated cell-cell communication using MeboCost for metabolic signaling inference between cell types. Predict…FreedomIntelligencescriptsbio-single-cell-splicingAnalyzes alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or leafcutter2 for…FreedomIntelligencescriptsbio-spatial-transcriptomics-image-analysisProcess and analyze tissue images from spatial transcriptomics data using Squidpy. Extract image features, segment cells/nuclei…FreedomIntelligencescriptsbio-spatial-transcriptomics-spatial-communicationAnalyze cell-cell communication in spatial transcriptomics data using ligand-receptor analysis with Squidpy. Infer intercellular…FreedomIntelligencescriptsbio-spatial-transcriptomics-spatial-data-ioLoad spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData.…FreedomIntelligencescriptsbio-spatial-transcriptomics-spatial-deconvolutionEstimate cell type composition in spatial transcriptomics spots using reference-based deconvolution. Use cell2location, RCTD…FreedomIntelligencescriptsbio-spatial-transcriptomics-spatial-domainsIdentify spatial domains and tissue regions in spatial transcriptomics data using Squidpy and Scanpy. Cluster spots considering…FreedomIntelligencescriptsbio-spatial-transcriptomics-spatial-neighborsBuild spatial neighbor graphs for spatial transcriptomics data using Squidpy. Compute k-nearest neighbors, Delaunay…FreedomIntelligencescriptsbio-spatial-transcriptomics-spatial-preprocessingQuality control, filtering, normalization, and feature selection for spatial transcriptomics data. Calculate QC metrics, filter…FreedomIntelligencescriptsbio-spatial-transcriptomics-spatial-proteomicsAnalyzes spatial proteomics data from CODEX, IMC, and MIBI platforms including cell segmentation and protein colocalization. Use…FreedomIntelligencescriptsbio-spatial-transcriptomics-spatial-statisticsCompute spatial statistics for spatial transcriptomics data using Squidpy. Calculate Moran's I, Geary's C, spatial…FreedomIntelligencescriptsbio-spatial-transcriptomics-spatial-visualizationVisualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and…FreedomIntelligencescriptsbio-splicing-qcAssesses RNA-seq data quality for splicing analysis including junction saturation curves, splice site strength scoring, and…FreedomIntelligencescriptsbio-splicing-quantificationQuantifies alternative splicing events (PSI/percent spliced in) from RNA-seq using SUPPA2 from transcript TPM or rMATS-turbo from…FreedomIntelligencescriptsbio-structural-biology-alphafold-predictionsAccess and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without…FreedomIntelligencescriptsbio-substructure-searchSearches molecular libraries for substructure matches using SMARTS patterns with RDKit. Filters compounds by pharmacophore…FreedomIntelligencescriptsbio-tcr-bcr-analysis-mixcr-analysisPerform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR. Use when processing raw immune…FreedomIntelligencescriptsbio-tcr-bcr-analysis-repertoire-visualizationCreate publication-quality visualizations of immune repertoire data including circos plots, clone tracking, diversity plots, and…FreedomIntelligencescriptsbio-tcr-bcr-analysis-scirpy-analysisAnalyze single-cell TCR and BCR data integrated with gene expression using scirpy. Use when working with 10x Genomics VDJ data…FreedomIntelligencescriptsbio-tcr-bcr-analysis-vdjtools-analysisCalculate immune repertoire diversity metrics, compare samples, and track clonal dynamics using VDJtools. Use when analyzing…FreedomIntelligencescriptsbio-variant-annotationComprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict…FreedomIntelligencescripts
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How the catalog works
What is an agent skill?

A folder with a SKILL.md inside — instructions, and often scripts and assets, that an AI agent loads when the task matches. Claude Code, Codex, Cursor and Copilot all read the same format, so one skill usually works across them.

Where does this catalog come from?

We read 660 source repositories straight from their file trees rather than from submitted listings — what you see is what is actually published. 98 repositories were rejected because they advertise skills but contain none: link lists, not folders.

Why is there no install counter?

Because install counts live in the registry that serves `npx skills add`, and that is not ours — publishing a number we cannot verify would be worse than showing none. Instead we show where a skill comes from and whether attention around its source is actually growing, measured from our own weekly snapshots.

Do you deduplicate?

Yes, and it matters more than expected. Aggregator repositories republish the same skill in several places — one source carried 6,317 SKILL.md files for 2,001 actual skills. We collapse by folder name and keep the canonical copy, so the catalog counts things, not copies.

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