Browse reusable Agent Skills, each with a clear purpose and practical guidance.
Load when summarising peptide identifications (PSM count, unique peptide count, distinct protein count, score / charge distributions) from a peptide-level CSV produced by MaxQuant / FragPipe / DIA-NN. Skip when raw spectra are the input (run a search engine first) or when working with protein-quantification tables (use `proteomics-ms-qc`).
Load when computing protein-table QC — proteins × samples count, missing-value rate, intensity CV (median + mean) — from a MaxQuant / FragPipe / DIA-NN protein-quantification CSV. Skip when raw mzML / RAW spectra are the input (run a search engine first) or when peptide-level QC is needed (use `proteomics-identification`).
Load when computing per-protein abundance from a peptide / PSM table via LFQ (intensity summation), iBAQ (intensity / tryptic peptide count), or spectral counting (PSMs per protein). Skip when the input is already protein-level (use `proteomics-ms-qc` for QC) or for label-based TMT / iTRAQ workflows (search upstream first).
Load when turning scRNA FASTQ (or existing CellRanger/STARsolo/SimpleAF/kb-python output) into a downstream-ready AnnData. Skip when reads are already counted into AnnData (use sc-standardize-input) or for raw quality assessment only (use sc-fastq-qc).
Load when removing low-quality cells and lowly-detected genes from a single-cell AnnData using QC-derived thresholds or tissue presets. Skip for the full normalize→HVG→PCA→cluster pipeline (use sc-preprocessing) or when reads are still raw FASTQ (use sc-fastq-qc → sc-count first).
Load when aggregating single cells into metacells (sample-aware coarse-grained pseudo-cells) on a normalised scRNA AnnData via SEACells or KMeans on a low-D embedding. Skip when ranking marker genes per cluster (use sc-markers) or for trajectory pseudotime ordering (use sc-pseudotime).
Load when attaching cell-barcode → sgRNA assignments from a mapping TSV/CSV onto a Perturb-seq expression AnnData, producing standardised perturbation / sgRNA / target-gene obs columns. Skip when the AnnData already has perturbation labels (go straight to sc-perturb) or for raw guide-calling from FASTQ (use upstream demuxlet / cellranger guide pipelines).
Load when normalising QC'd scRNA into a PCA-ready AnnData via scanpy / Seurat / SCTransform / Pearson residuals. Skip when QC thresholds are still undecided (use sc-qc) or for batch correction across samples (use sc-batch-integration).
Load when preprocessing a single-cell ATAC peak × cell AnnData via Signac-style TF-IDF + LSI + Leiden, producing a clustered UMAP-ready object. Skip when input is fragments or BAM (peak calling not implemented here) or for scRNA preprocessing (use sc-preprocessing).
Load when deconvolving spot-level cell-type proportions on a Visium-style spatial AnnData using a labelled scRNA reference (FlashDeconv / Cell2location / RCTD / DestVI / Tangram / others). Skip when each spot is a single cell already (Xenium / MERFISH — use spatial-annotate) or for tissue-domain detection (use spatial-domains).