omics-tools

What problem does it solve?

This Skill helps users quickly inspect and triage various omics datasets (single-cell, alignment, mass-spectrometry) before diving into complex downstream analysis, ensuring data readiness and identifying potential issues early.

Core Features & Use Cases

• AnnData Profiling: Summarize cell types, batch information, and QC metrics from h5ad files using Scanpy-style checks.
• Alignment Inspection: Profile BAM/CRAM files for read counts, mapped/unmapped statistics, and region-specific coverage using pysam.
• Mass-Spectrometry Triage: Inventory mzML files for spectra counts, MS levels, and retention time ranges using pyOpenMS.
• Use Case: Before running a differential expression analysis on single-cell RNA-seq data, use this Skill to get a quick overview of cell type distributions and batch effects in your h5ad file.

Quick Start

Use the omics-tools skill to profile the AnnData file 'data/pbmc.h5ad', checking for 'cell_type' and 'batch' columns.