80,000+ Skills to Supercharge Claude
The open directory for GitHub-integrated capabilities, tools, and prompts for your AI workflows.
bio-atac-seq-atac-qc
by GPTomics
Quality control metrics for ATAC-seq data including fragment size distribution, TSS enrichment, FRiP, and library comple...
bio-variant-calling-filte...
by GPTomics
Comprehensive variant filtering including GATK VQSR, hard filters, bcftools expressions, and quality metric interpretati...
bio-flow-cytometry-double...
by GPTomics
Detect and remove doublets from flow and mass cytometry data. Covers FSC/SSC gating and computational doublet detection...
bio-microbiome-differenti...
by GPTomics
Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsL...
bio-data-visualization-he...
by GPTomics
Create clustered heatmaps with row/column annotations using ComplexHeatmap, pheatmap, and seaborn for gene expression an...
bio-variant-normalization
by GPTomics
Normalize indel representation and split multiallelic variants using bcftools norm. Use when comparing variants from dif...
bio-microbiome-amplicon-p...
by GPTomics
Amplicon sequence variant (ASV) inference from 16S rRNA or ITS amplicon sequencing using DADA2. Covers quality filtering...
bio-workflows-microbiome-...
by GPTomics
End-to-end 16S amplicon workflow from FASTQ reads to differential abundance. Orchestrates DADA2 ASV inference, taxonomy...
bio-metagenomics-kraken
by GPTomics
Taxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database. Us...
bio-genome-intervals-inte...
by GPTomics
Core interval arithmetic operations including intersect, subtract, merge, complement, map, and groupby using bedtools an...
bio-alignment-indexing
by GPTomics
Create and use BAI/CSI indices for BAM/CRAM files using samtools and pysam. Use when enabling random access to alignment...
bio-read-alignment-bowtie...
by GPTomics
Align short reads using Bowtie2 with local or end-to-end modes. Use for ChIP-seq, ATAC-seq, or when you need flexible al...
bio-microbiome-taxonomy-a...
by GPTomics
Taxonomic classification of ASVs using reference databases like SILVA, GTDB, or UNITE. Covers naive Bayes classifiers (D...
bio-atac-seq-nucleosome-p...
by GPTomics
Extract nucleosome positions from ATAC-seq data using NucleoATAC, ATACseqQC, and fragment analysis. Use when analyzing c...
bio-differential-expressi...
by GPTomics
Analyze time-series RNA-seq data using limma voom with splines, maSigPro, and ImpulseDE2. Identify genes with dynamic ex...
bio-proteomics-proteomics...
by GPTomics
Quality control and assessment for proteomics data. Covers sample quality metrics, missing value patterns, replicate cor...
bio-crispr-batch-correcti...
by GPTomics
Batch effect correction for CRISPR screens. Covers normalization across batches, technical replicate handling, and batch...
bio-workflows-atacseq-pip...
by GPTomics
End-to-end ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting. Covers alignment, peak...
bio-multi-omics-mixomics-...
by GPTomics
Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for...
bio-population-genetics-a...
by GPTomics
Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using...
bio-phasing-imputation-im...
by GPTomics
Quality control of phasing and imputation results. Filter by INFO scores, assess accuracy, and prepare imputed data for...
bio-variant-calling
by GPTomics
Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or g...
bio-workflows-multi-omics...
by GPTomics
End-to-end multi-omics integration workflow. Orchestrates data harmonization, MOFA/mixOmics integration, factor interpre...
bio-rna-quantification-tx...
by GPTomics
Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using txim...