gptomics/bioskills

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bioskills Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, s…

gptomics/bioskills

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clawhub-installer Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, s…

gptomics/bioskills

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bio-single-cell-batch-integration Integrate multiple scRNA-seq samples or batches with Harmony, scVI/scANVI, Seurat (CCA/RPCA), fastMNN, Scanorama, or …

gptomics/bioskills

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bio-workflows-rnaseq-to-de Orchestrates the end-to-end bulk RNA-seq differential-expression pipeline from FASTQ to an annotated DE gene table, c…

gptomics/bioskills

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bio-workflows-scrnaseq-pipeline Orchestrates the end-to-end single-cell RNA-seq pipeline from 10x Cell Ranger output to annotated cell types, chainin…

gptomics/bioskills

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bio-data-visualization-genome-tracks Create genome browser-style visualizations showing multiple data tracks (coverage, peaks, genes) using pyGenomeTracks…

gptomics/bioskills

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bio-data-visualization-multipanel-figures Combine multiple plots into publication-ready multi-panel figures using patchwork, cowplot, or matplotlib GridSpec wi…

gptomics/bioskills

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bio-data-visualization-specialized-omics-plots Reusable plotting functions for common omics visualizations. Custom ggplot2/matplotlib implementations of volcano, MA…

gptomics/bioskills

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bio-epitranscriptomics-merip-preprocessing Align and QC MeRIP-seq IP and input samples for m6A analysis. Use when preparing MeRIP-seq data for peak calling or d…

gptomics/bioskills

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bio-expression-matrix-metadata-joins Aligns sample metadata with count matrices and constructs design matrices for downstream DE, handling the alphabetica…

gptomics/bioskills

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bio-metagenomics-kraken Taxonomic classification of metagenomic reads using Kraken2. Fast k-mer based classification against RefSeq database.…

gptomics/bioskills

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bio-pathway-enrichment-visualization Turns an enrichResult or gseaResult from clusterProfiler/enrichplot into a figure that collapses or shows gene-set re…

gptomics/bioskills

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bio-pathway-go-enrichment Runs Gene Ontology over-representation analysis (ORA) on a gene LIST with clusterProfiler enrichGO, the one-sided hyp…

gptomics/bioskills

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bio-pathway-reactome Tests a gene list or ranked gene vector for over-representation or coordinated shifts in Reactome's curated, peer-rev…

gptomics/bioskills

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bio-read-qc-fastp-workflow All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correctio…

gptomics/bioskills

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bio-rna-quantification-count-matrix-qc Quality control and exploration of RNA-seq count matrices before differential expression. Use when checking library s…

gptomics/bioskills

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bio-single-cell-multimodal-integration Integrate multimodal single-cell data (CITE-seq RNA+protein, 10x Multiome RNA+ATAC, unpaired/diagonal RNA+ATAC) and c…

gptomics/bioskills

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bio-workflows-microbiome-pipeline End-to-end 16S amplicon workflow from FASTQ reads to differential abundance. Orchestrates DADA2 ASV inference, taxono…

gptomics/bioskills

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bio-data-visualization-circos-plots Create circular genome visualizations with Circos and pyCircos. Display multi-track data including ideograms, genes, …

gptomics/bioskills

4

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bio-data-visualization-color-palettes Select and apply colorblind-friendly palettes for scientific figures using viridis, RColorBrewer, and custom color sc…

gptomics/bioskills

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bio-data-visualization-ggplot2-fundamentals Create publication-quality scientific figures with ggplot2 including scatter plots, boxplots, heatmaps, and multi-pan…

gptomics/bioskills

4

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bio-data-visualization-heatmaps-clustering Create clustered heatmaps with row/column annotations using ComplexHeatmap, pheatmap, and seaborn for gene expression…

gptomics/bioskills

4

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bio-de-deseq2-basics Perform differential expression analysis using DESeq2 in R/Bioconductor. Use for analyzing RNA-seq count data, creati…

gptomics/bioskills

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bio-de-visualization Visualize differential expression results using DESeq2/edgeR built-in functions. Covers plotMA, plotDispEsts, plotCou…

gptomics/bioskills

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bio-differential-expression-batch-correction Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for vi…

gptomics/bioskills

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bio-differential-expression-timeseries-de Analyzes time-series and longitudinal RNA-seq for differential expression and trajectory structure. Covers DESeq2 LRT…

gptomics/bioskills

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bio-epitranscriptomics-m6a-differential Identify differential m6A methylation between conditions from MeRIP-seq. Use when comparing epitranscriptomic changes…

gptomics/bioskills

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bio-epitranscriptomics-m6a-peak-calling Call m6A peaks from MeRIP-seq IP vs input comparisons. Use when identifying m6A modification sites from methylated RN…

gptomics/bioskills

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bio-epitranscriptomics-modification-visualization Create metagene plots and browser tracks for RNA modification data. Use when visualizing m6A distribution patterns ar…

gptomics/bioskills

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bio-expression-matrix-counts-ingest Imports gene expression count matrices from featureCounts, HTSeq, STAR ReadsPerGene, Salmon/kallisto via tximport or …

gptomics/bioskills

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bio-expression-matrix-gene-id-mapping Maps between gene identifier systems (Ensembl, Entrez, HGNC symbol, UniProt, RefSeq, MANE) using AnnotationDbi, bioma…

gptomics/bioskills

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bio-expression-matrix-sparse-handling Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatri…

gptomics/bioskills

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bio-genome-assembly-contamination-detection Detect contamination and assess genome quality using CheckM, CheckM2, GTDB-Tk, and GUNC for metagenome-assembled geno…

gptomics/bioskills

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bio-genome-intervals-gtf-gff-handling Parse, query, and convert GTF and GFF3 annotation files. Extract gene, transcript, and exon coordinates using gffread…

gptomics/bioskills

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bio-longread-alignment Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read type…

gptomics/bioskills

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bio-methylation-bismark-alignment Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM fi…

gptomics/bioskills

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bio-microbiome-diversity-analysis Alpha and beta diversity analysis for microbiome data. Calculate within-sample richness, evenness, and between-sample…

gptomics/bioskills

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bio-pathway-gsea Tests a ranked gene vector for coordinated expression shifts in GO, KEGG, Reactome, or MSigDB gene sets with clusterP…

gptomics/bioskills

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bio-pathway-kegg-pathways Tests gene lists, ranked vectors, and fold-change vectors against KEGG pathways and modules with clusterProfiler enri…

gptomics/bioskills

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bio-pathway-wikipathways Tests a gene list (ORA, enrichWP) or a ranked gene vector (GSEA, gseWP) against the WikiPathways community-curated pa…

gptomics/bioskills

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bio-reporting-rmarkdown-reports Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HT…

gptomics/bioskills

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bio-rna-quantification-alignment-free-quant Quantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with …

gptomics/bioskills

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bio-rnaseq-qc RNA-seq specific quality control including rRNA contamination detection, strandedness verification, gene body coverag…

gptomics/bioskills

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bio-single-cell-cell-annotation Automated reference-based cell type annotation for single-cell RNA-seq using CellTypist, SingleR, Azimuth, scANVI, an…

gptomics/bioskills

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bio-single-cell-cell-communication Infers ligand-receptor cell-cell communication from scRNA-seq with a consensus-first workflow (LIANA), plus CellPhone…

gptomics/bioskills

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bio-single-cell-clustering Dimensionality reduction and graph-based clustering for single-cell RNA-seq with Scanpy (Python) and Seurat (R). Reso…

gptomics/bioskills

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bio-single-cell-data-io Read, write, create, and convert single-cell objects across AnnData (Python), Seurat (R), and SingleCellExperiment (R…

gptomics/bioskills

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bio-single-cell-doublet-detection Detect and remove doublets (two or more cells in one droplet) from single-cell RNA-seq using scDblFinder (R), Scruble…

gptomics/bioskills

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bio-single-cell-lineage-tracing Reconstructs single-cell lineage trees and clonal relationships from CRISPR/Cas9 scars, static expressed barcodes (LA…

gptomics/bioskills

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bio-single-cell-markers-annotation Detect cluster marker genes and assign manual cell type labels in single-cell RNA-seq using Scanpy (Python) and Seura…

gptomics/bioskills

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