80,000+ Skills to Supercharge Claude
The open directory for GitHub-integrated capabilities, tools, and prompts for your AI workflows.
bio-long-read-sequencing-...
by GPTomics
Deep learning-based variant calling from long reads using Clair3 for SNPs and small indels. Use when calling germline va...
bio-vcf-statistics
by GPTomics
Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck. Use when evaluati...
bio-duplicate-handling
by GPTomics
Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant cal...
bio-gatk-variant-calling
by GPTomics
Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for...
bio-metagenomics-abundanc...
by GPTomics
Species abundance estimation using Bracken with Kraken2 output. Redistributes reads from higher taxonomic levels to spec...
bio-single-cell-cell-anno...
by GPTomics
Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for cons...
bio-de-visualization
by GPTomics
Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCounts...
bio-metagenomics-metaphla...
by GPTomics
Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade...
bio-genome-assembly-long-...
by GPTomics
De novo genome assembly from Oxford Nanopore or PacBio long reads using Flye and Canu. Produces highly contiguous assemb...
bio-restriction-sites
by GPTomics
Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Search with single enzymes, batches...
bio-genome-assembly-scaff...
by GPTomics
Scaffold contigs into chromosome-level assemblies using Hi-C data with YaHS, 3D-DNA, SALSA2, and validate with BUSCO and...
bio-genome-assembly-assem...
by GPTomics
Polish genome assemblies to reduce errors using short reads (Pilon), long reads (Racon), or ONT-specific tools (medaka)....
bio-proteomics-peptide-id...
by GPTomics
Peptide-spectrum matching and protein identification from MS/MS data. Covers database searching, spectral library matchi...
bio-write-sequences
by GPTomics
Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences,...
bio-workflows-metagenomic...
by GPTomics
End-to-end metagenomics workflow from FASTQ to taxonomic and functional profiles. Covers Kraken2 classification, Bracken...
bio-proteomics-dia-analys...
by GPTomics
Data-independent acquisition (DIA) proteomics analysis with DIA-NN and other tools. Covers library-free and library-base...
bio-crispr-screens-screen...
by GPTomics
Quality control for pooled CRISPR screens. Covers library representation, read distribution, replicate correlation, and...
bio-workflows-imc-pipelin...
by GPTomics
End-to-end imaging mass cytometry workflow from raw acquisitions to spatial cell analysis. Orchestrates image preprocess...
bio-spatial-transcriptomi...
by GPTomics
Visualize spatial transcriptomics data using Squidpy and Scanpy. Create tissue plots with gene expression, clusters, and...
bio-workflows-scrnaseq-pi...
by GPTomics
End-to-end single-cell RNA-seq workflow from 10X Genomics data to annotated cell types. Covers QC, normalization, cluste...
bio-read-qc-umi-processin...
by GPTomics
Extract, process, and deduplicate reads using Unique Molecular Identifiers (UMIs) with umi_tools. Use when library prep...
bio-pathway-enrichment-vi...
by GPTomics
Visualize enrichment results using enrichplot package functions. Covers dotplot, barplot, cnetplot, emapplot, gseaplot2,...
bio-phylo-tree-io
by GPTomics
Read, write, and convert phylogenetic tree files using Biopython Bio.Phylo. Use for parsing Newick, Nexus, PhyloXML, and...
bio-workflows-longread-sv...
by GPTomics
End-to-end workflow for detecting structural variants from long-read sequencing data. Covers ONT/PacBio alignment with m...