GitHub
bio-workflows-atacseq-pipeline
End-to-end ATAC-seq workflow from FASTQ files to differential accessibility and TF footprinting. Covers alignment, peak calling with MACS3, QC metrics, and optional TOBIAS footprinting.
☆ 300View skill
GPTomics AI Skills
GitHub ↗Browse published AI skills maintained by GPTomics. Compare skill descriptions and follow each source repository for setup instructions.
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Indexed skills
269Repository stars across indexed skills
80,661Repository forks
13,719Average repository stars per indexed skill
300Repository stars may repeat across skills from the same repository.
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GitHub
bio-multi-omics-mixomics-analysis
Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for multi-block discriminant analysis.
☆ 300View skill
GitHub
bio-population-genetics-association-testing
Genome-wide association studies (GWAS) with PLINK. Perform case-control and quantitative trait association testing using logistic/linear regression with covariates, generate Manhattan and QQ plots for result vi...
☆ 300View skill
GitHub
bio-phasing-imputation-imputation-qc
Quality control of phasing and imputation results. Filter by INFO scores, assess accuracy, and prepare imputed data for downstream analysis. Use when filtering low-quality imputed variants or validating imputat...
☆ 300View skill
GitHub
bio-variant-calling
Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.
☆ 300View skill
GitHub
bio-workflows-multi-omics-pipeline
End-to-end multi-omics integration workflow. Orchestrates data harmonization, MOFA/mixOmics integration, factor interpretation, and downstream analysis across transcriptomics, proteomics, metabolomics, and othe...
☆ 300View skill
GitHub
bio-rna-quantification-tximport-workflow
Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta.
☆ 300View skill
GitHub
bio-flow-cytometry-clustering-phenotyping
Unsupervised clustering and cell type identification for flow/mass cytometry. Covers FlowSOM, Phenograph, and CATALYST workflows. Use when discovering cell populations in high-dimensional cytometry data without...
☆ 300View skill
GitHub
bio-alignment-statistics
Generate alignment statistics using samtools flagstat, stats, depth, and coverage. Use when assessing alignment quality, calculating coverage, or generating QC reports.
☆ 300View skill
GitHub
bio-longread-medaka
Polish assemblies and call variants from Oxford Nanopore data using medaka. Uses neural networks trained on specific basecaller versions. Use when improving ONT-only assemblies or calling variants from Nanopore...
☆ 300View skill
GitHub
bio-phasing-imputation-reference-panels
Download, prepare, and manage reference panels for phasing and imputation. Covers 1000 Genomes, HRC, and TOPMed panels. Use when setting up imputation infrastructure or selecting appropriate reference panels fo...
☆ 300View skill
GitHub
bio-read-qc-fastp-workflow
All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML report generation. Use when preprocessing Illumina data and wanting a single fast...
☆ 300View skill
GitHub
bio-alignment-filtering
Filter alignments by flags, mapping quality, and regions using samtools view and pysam. Use when extracting specific reads, removing low-quality alignments, or subsetting to target regions.
☆ 300View skill
GitHub
bio-reference-operations
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionaries.
☆ 300View skill
GitHub
bio-imc-interactive-annotation
Interactive cell type annotation for IMC data. Covers napari-based annotation, marker-guided labeling, training data generation, and annotation validation. Use when manually annotating cell types for training c...
☆ 300View skill
GitHub
bio-workflows-chipseq-pipeline
End-to-end ChIP-seq workflow from FASTQ files to annotated peaks. Covers QC, alignment, peak calling with MACS3, and peak annotation with ChIPseeker.
☆ 300View skill
GitHub
bio-single-cell-trajectory-inference
Infer developmental trajectories and pseudotime from single-cell RNA-seq data using Monocle3, Slingshot, and scVelo for RNA velocity analysis.
☆ 300View skill
GitHub
bio-methylation-dmr-detection
Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation differences between experimental conditions o...
☆ 300View skill
GitHub
bio-flow-cytometry-cytometry-qc
Comprehensive quality control for flow cytometry and CyTOF data. Covers flow rate stability, signal drift, margin events, dead cell exclusion, and batch QC. Use when assessing acquisition quality or identifying...
☆ 300View skill
GitHub
bio-expression-matrix-sparse-handling
Work with sparse matrices for memory-efficient storage of count data. Use when dealing with single-cell data or large bulk RNA-seq datasets where most values are zero.
☆ 300View skill
GitHub
bio-copy-number-gatk-cnv
Call copy number variants using GATK best practices workflow. Supports both somatic (tumor-normal) and germline CNV detection from WGS or WES data. Use when following GATK best practices or integrating CNV call...
☆ 300View skill
GitHub
bio-multi-omics-similarity-network
Similarity Network Fusion (SNF) for patient stratification using multi-omics data. Integrates multiple data types into a unified patient similarity network.
☆ 300View skill
GitHub
bio-genome-intervals-proximity-operations
Find nearest features, search within windows, and extend intervals using closest, window, flank, and slop operations. Use when performing TSS proximity analysis, assigning enhancers to genes, defining promoter...
☆ 300View skill
GitHub
bio-chip-seq-super-enhancers
Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools. Use when studying cell identity genes, cancer-associated regulatory elements, or master transcription factor binding regions t...
☆ 300View skill
The default order uses GitHub repository stars from our indexed data. Stars belong to the source repository and may be shared by multiple skills. They indicate repository interest, not skill installs or an independent quality score.