Scanpy · GPTomics/bioSkills

Produce and interpret PCA, t-SNE, UMAP, and PHATE plots for high-dimensional omics data with rigor about which method preserves what (variance, local structure, manifold, transitions)…

GPTomics/bioSkills

Reads, inspects, and writes Flow Cytometry Standard (FCS) files from conventional, spectral, and mass cytometry (CyTOF), and parses FlowJo/Cytobank/Diva workspaces.

GPTomics/bioSkills

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

GPTomics/bioSkills

Detect cluster marker genes and assign manual cell type labels in single-cell RNA-seq using Scanpy (Python) and Seurat (R).

GPTomics/bioSkills

Quality control, ambient-RNA handling, normalization, and feature selection for single-cell RNA-seq using Scanpy (Python) and Seurat (R).

GPTomics/bioSkills

Quality control, filtering, and normalization for spatial transcriptomics (Visium, Visium HD, Xenium, MERFISH/MERSCOPE, CosMx, Slide-seq) with Squidpy and Scanpy.

GPTomics/bioSkills

Plots spatial transcriptomics expression, clusters, and annotations on tissue using Squidpy and Scanpy.

GPTomics/bioSkills

Orchestrates the end-to-end spatial transcriptomics pipeline from Space Ranger / vendor output to spatial domains and statistics, branching FIRST on platform class (imaging in-situ…

GPTomics/bioSkills

Normalizes and transforms RNA-seq count matrices for DE, visualization, clustering, and ML.

GPTomics/bioSkills

Stores and operates on sparse expression matrices for single-cell and large bulk RNA-seq, covering dgCMatrix/dgRMatrix/dgTMatrix when-each-is-fast, the dgCMatrix (CSC, R) <- CSR (Python) implicit…

GPTomics/bioSkills