80,000+ Skills to Supercharge Claude
The open directory for GitHub-integrated capabilities, tools, and prompts for your AI workflows.
bio-flow-cytometry-cluste...
by GPTomics
Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST w...
bio-alignment-statistics
by GPTomics
Generate alignment statistics using samtools flagstat, stats, depth, and coverage. Use when assessing alignment quality,...
bio-longread-medaka
by GPTomics
Polish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific bas...
bio-phasing-imputation-re...
by GPTomics
Download, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels....
bio-read-qc-fastp-workflo...
by GPTomics
All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction,...
bio-alignment-filtering
by GPTomics
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific rea...
bio-reference-operations
by GPTomics
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, ind...
bio-imc-interactive-annot...
by GPTomics
Interactive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data gen...
bio-workflows-chipseq-pip...
by GPTomics
End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and pea...
bio-single-cell-trajector...
by GPTomics
Infer developmental trajectories and pseudotime from single-cell RNA-seq data using Monocle3, Slingshot, and scVelo for...
bio-methylation-dmr-detec...
by GPTomics
Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying...
bio-flow-cytometry-cytome...
by GPTomics
Comprehensive quality control for flow cytometry and CyTOF data. Covers flow rate stability, signal drift, margin events...
bio-expression-matrix-spa...
by GPTomics
Work with sparse matrices for memory-efficient storage of count data. Use when dealing with single-cell data or large bu...
bio-copy-number-gatk-cnv
by GPTomics
Call copy number variants using GATK best practices workflow. Supports both somatic (tumor-normal) and germline CNV dete...
bio-multi-omics-similarit...
by GPTomics
Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a...
bio-genome-intervals-prox...
by GPTomics
Find nearest features, search within windows, and extend intervals using closest, window, flank, and slop operations. Us...
bio-chip-seq-super-enhanc...
by GPTomics
Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. Use when studying cell identity gene...
bio-workflows-gwas-pipeli...
by GPTomics
End-to-end GWAS workflow from VCF to association results. Covers PLINK QC, population structure correction, and associat...
bio-genome-assembly-metag...
by GPTomics
Metagenome assembly from long reads using metaFlye and metaSPAdes with binning strategies. Use when reconstructing genom...
bio-single-cell-doublet-d...
by GPTomics
Detect and remove doublets (multiple cells captured in one droplet) from single-cell RNA-seq data. Uses Scrublet (Python...
bio-variant-calling-struc...
by GPTomics
Call structural variants (SVs) from short-read sequencing using Manta, Delly, and LUMPY. Detects deletions, insertions,...
bio-spatial-transcriptomi...
by GPTomics
Estimate cell type composition in spatial transcriptomics spots using reference-based deconvolution. Use cell2location,...
bio-methylation-bismark-a...
by GPTomics
Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files...
bio-multi-omics-data-harm...
by GPTomics
Preprocessing and harmonization of multi-omics data before integration. Covers normalization, batch correction, feature...