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
2,3532,400 · page 50 / 1,306
bio-epidemiological-genomics-amr-surveillanceDetect and track antimicrobial resistance genes using AMRFinderPlus and ResFinder with epidemiological context. Monitor…FreedomIntelligencescriptsbio-epidemiological-genomics-pathogen-typingPerform multi-locus sequence typing (MLST), core genome MLST, and SNP-based strain typing for bacterial isolate characterization…FreedomIntelligencescriptsbio-epidemiological-genomics-phylodynamicsConstruct time-scaled phylogenies and infer evolutionary dynamics using TreeTime and BEAST2 for outbreak analysis. Estimate…FreedomIntelligencescriptsbio-epidemiological-genomics-transmission-inferenceInfer pathogen transmission networks and identify likely transmission pairs using TransPhylo and outbreak reconstruction…FreedomIntelligencescriptsbio-epidemiological-genomics-variant-surveillanceAssign pathogen lineages and track variants using Nextclade and pangolin for viral surveillance. Monitor variant prevalence and…FreedomIntelligencescriptsbio-fastq-qualityWork with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality…FreedomIntelligencescriptsbio-filter-sequencesFilter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences…FreedomIntelligencescriptsbio-format-conversionConvert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or…FreedomIntelligencescriptsbio-fragment-analysisAnalyzes cfDNA fragment size distributions and fragmentomics features using FinaleToolkit or Griffin. Extracts nucleosome…FreedomIntelligencescriptsbio-genome-engineering-base-editing-designDesign guides for cytosine and adenine base editing using editing window optimization and BE-Hive outcome prediction. Select…FreedomIntelligencescriptsbio-genome-engineering-grna-designDesign guide RNAs for CRISPR-Cas9/Cas12a experiments using CRISPRscan and local scoring algorithms. Score guides for on-target…FreedomIntelligencescriptsbio-genome-engineering-hdr-template-designDesign homology-directed repair donor templates for CRISPR knock-ins using primer3-py. Create ssODN, dsDNA, or plasmid templates…FreedomIntelligencescriptsbio-genome-engineering-off-target-predictionPredict CRISPR off-target sites using Cas-OFFinder and CFD scoring algorithms. Identify potential unintended cleavage sites…FreedomIntelligencescriptsbio-genome-engineering-prime-editing-designDesign pegRNAs for prime editing using PrimeDesign algorithms. Generate spacer, PBS, and RT template sequences for precise…FreedomIntelligencescriptsbio-hi-c-analysis-compartment-analysisDetect A/B compartments from Hi-C data using cooltools and eigenvector decomposition. Identify active (A) and inactive (B)…FreedomIntelligencescriptsbio-hi-c-analysis-contact-pairsProcess Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics…FreedomIntelligencescriptsbio-hi-c-analysis-hic-data-ioLoad, convert, and manipulate Hi-C contact matrices using cooler format. Read .cool/.mcool files, convert from .hic format…FreedomIntelligencescriptsbio-hi-c-analysis-hic-differentialCompare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes…FreedomIntelligencescriptsbio-hi-c-analysis-hic-visualizationVisualize Hi-C contact matrices, TADs, loops, and genomic features using matplotlib, cooltools, and HiCExplorer. Create triangle…FreedomIntelligencescriptsbio-hi-c-analysis-loop-callingDetect chromatin loops and point interactions from Hi-C data using cooltools, chromosight, and HiCCUPS-like methods. Identify…FreedomIntelligencescriptsbio-hi-c-analysis-matrix-operationsBalance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute…FreedomIntelligencescriptsbio-hi-c-analysis-tad-detectionCall topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify…FreedomIntelligencescriptsbio-imaging-mass-cytometry-cell-segmentationCell segmentation from multiplexed tissue images. Covers deep learning (Cellpose, Mesmer) and classical approaches for nuclear…FreedomIntelligencescriptsbio-imaging-mass-cytometry-data-preprocessingLoad and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image…FreedomIntelligencescriptsbio-imaging-mass-cytometry-interactive-annotationInteractive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation…FreedomIntelligencescriptsbio-imaging-mass-cytometry-phenotypingCell type assignment from marker expression in IMC data. Covers manual gating, clustering, and automated classification…FreedomIntelligencescriptsbio-imaging-mass-cytometry-quality-metricsQuality metrics for IMC data including signal-to-noise, channel correlation, tissue integrity, and acquisition QC. Use when…FreedomIntelligencescriptsbio-imaging-mass-cytometry-spatial-analysisSpatial analysis of cell neighborhoods and interactions in IMC data. Covers neighbor graphs, spatial statistics, and interaction…FreedomIntelligencescriptsbio-immunoinformatics-epitope-predictionPredict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody design.…FreedomIntelligencescriptsbio-immunoinformatics-immunogenicity-scoringScore and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing…FreedomIntelligencescriptsbio-immunoinformatics-mhc-binding-predictionPredict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potential…FreedomIntelligencescriptsbio-immunoinformatics-neoantigen-predictionIdentify tumor neoantigens from somatic mutations using pVACtools for personalized cancer immunotherapy. Predict mutant peptides…FreedomIntelligencescriptsbio-immunoinformatics-tcr-epitope-bindingPredict TCR-epitope specificity using ERGO-II and deep learning models for T-cell receptor antigen recognition. Match TCRs to…FreedomIntelligencescriptsbio-long-read-sequencing-clair3-variantsDeep learning-based variant calling from long reads using Clair3 for SNPs and small indels. Use when calling germline variants…FreedomIntelligencescriptsbio-long-read-sequencing-nanopore-methylationCalls DNA methylation from Oxford Nanopore sequencing data using signal-level analysis. Use when detecting 5mC or 6mA…FreedomIntelligencescriptsbio-longitudinal-monitoringTracks ctDNA dynamics over time for treatment response monitoring using serial liquid biopsy samples. Analyzes tumor fraction…FreedomIntelligencescriptsbio-longread-alignmentAlign long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and…FreedomIntelligencescriptsbio-longread-qcQuality control for long-read sequencing data using NanoPlot, NanoStat, and chopper. Generate QC reports, filter reads by length…FreedomIntelligencescriptsbio-longread-structural-variantsDetect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, insertions…FreedomIntelligencescriptsbio-metabolomics-metabolite-annotationMetabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level…FreedomIntelligencescriptsbio-metagenomics-abundanceSpecies abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to species for…FreedomIntelligencescriptsbio-metagenomics-functional-profilingProfile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family…FreedomIntelligencescriptsbio-metagenomics-krakenTaxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database. Use when…FreedomIntelligencescriptsbio-metagenomics-metaphlanMarker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific…FreedomIntelligencescriptsbio-methylation-based-detectionAnalyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bisulfite sequencing with MethylDackel. Identifies…FreedomIntelligencescriptsbio-methylation-bismark-alignmentBisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with…FreedomIntelligencescriptsbio-methylation-callingExtract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG…FreedomIntelligencescriptsbio-microbiome-functional-predictionPredict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundances from…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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