80,000+ Skills to Supercharge Claude
The open directory for GitHub-integrated capabilities, tools, and prompts for your AI workflows.
bio-compressed-files
by GPTomics
Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with .gz or .bz2 sequence...
bio-flow-cytometry-compen...
by GPTomics
Spillover compensation and data transformation for flow cytometry. Covers compensation matrix calculation, application,...
bio-population-genetics-p...
by GPTomics
Analyze population structure using PCA and admixture analysis with PLINK and ADMIXTURE. Identify population clusters, as...
bio-vcf-basics
by GPTomics
View, query, and understand VCF/BCF variant files using bcftools and cyvcf2. Use when inspecting variants, extracting sp...
bio-single-cell-batch-int...
by GPTomics
Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variatio...
bio-microbiome-diversity-...
by GPTomics
Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample di...
bio-chipseq-qc
by GPTomics
ChIP-seq quality control metrics including FRiP (Fraction of Reads in Peaks), cross-correlation analysis (NSC/RSC), libr...
bio-rna-quantification-co...
by GPTomics
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effe...
bio-longread-structural-v...
by GPTomics
Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, ins...
bio-alignment-io
by GPTomics
Read, write, and convert multiple sequence alignment files using Biopython Bio.AlignIO. Supports Clustal, PHYLIP, Stockh...
bio-single-cell-scatac-an...
by GPTomics
Single-cell ATAC-seq analysis with Signac (R/Seurat) and ArchR. Process 10X Genomics scATAC data, perform QC, dimensiona...
bio-consensus-sequences
by GPTomics
Generate consensus FASTA sequences by applying VCF variants to a reference using bcftools consensus. Use when creating s...
bio-pileup-generation
by GPTomics
Generate pileup data for variant calling using samtools mpileup and pysam. Use when preparing data for variant calling,...
bio-read-qc-quality-filte...
by GPTomics
Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove...
bio-variant-calling-joint...
by GPTomics
Joint genotype calling across multiple samples using GATK CombineGVCFs and GenotypeGVCFs. Essential for cohort studies,...
bio-phylo-tree-manipulati...
by GPTomics
Modify phylogenetic tree structure using Biopython Bio.Phylo. Use for rooting trees with outgroups or midpoint, pruning...
bio-atac-seq-footprinting
by GPTomics
Detect transcription factor binding sites through footprinting analysis in ATAC-seq data using TOBIAS. Use when identify...
bio-reverse-complement
by GPTomics
Generate reverse complements and complements of DNA/RNA sequences using Biopython. Use when working with opposite strand...
bio-spatial-transcriptomi...
by GPTomics
Build spatial neighbor graphs for spatial transcriptomics data using Squidpy. Compute k-nearest neighbors, Delaunay tria...
bio-hi-c-analysis-hic-dif...
by GPTomics
Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold chan...
bio-workflows-somatic-var...
by GPTomics
End-to-end somatic variant calling from tumor-normal paired samples using Mutect2 or Strelka2. Covers preprocessing, var...
bio-imaging-mass-cytometr...
by GPTomics
Load and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image n...
bio-phasing-imputation-ge...
by GPTomics
Impute missing genotypes using reference panels with Beagle or Minimac4. Use when increasing variant density for GWAS, h...
bio-read-qc-adapter-trimm...
by GPTomics
Remove sequencing adapters from FASTQ files using Cutadapt and Trimmomatic. Supports single-end and paired-end reads, Il...