exploratory-data-analysis

# Exploratory Data Analysis ## Overview Perform comprehensive exploratory data analysis (EDA) on scientific data files across multiple domains. This skill provides automated file type detection, format-specific analysis, data quality assessment, and generates detailed markdown reports suitable for documentation and downstream analysis planning. **Key Capabilities:** - Automatic detection and analysis of 200+ scientific file formats - Comprehensive format-specific metadata extraction - Data quality and integrity assessment - Statistical summaries and distributions - Visualization recommendations - Downstream analysis suggestions - Markdown report generation ## When to Use This Skill Use this skill when: - User provides a path to a scientific data file for analysis - User asks to "explore", "analyze", or "summarize" a data file - User wants to understand the structure and content of scientific data - User needs a comprehensive report of a dataset before analysis - User wants to assess data quality or completeness - User asks what type of analysis is appropriate for a file ## Supported File Categories The skill has comprehensive coverage of scientific file formats organized into six major categories: ### 1. Chemistry and Molecular Formats (60+ extensions) Structure files, computational chemistry outputs, molecular dynamics trajectories, and chemical databases. **File types include:** `.pdb`, `.cif`, `.mol`, `.mol2`, `.sdf`, `.xyz`, `.smi`, `.gro`, `.log`, `.fchk`, `.cube`, `.dcd`, `.xtc`, `.trr`, `.prmtop`, `.psf`, and more. **Reference file:** `references/chemistry_molecular_formats.md` ### 2. Bioinformatics and Genomics Formats (50+ extensions) Sequence data, alignments, annotations, variants, and expression data. **File types include:** `.fasta`, `.fastq`, `.sam`, `.bam`, `.vcf`, `.bed`, `.gff`, `.gtf`, `.bigwig`, `.h5ad`, `.loom`, `.counts`, `.mtx`, and more. **Reference file:** `references/bioinformatics_genomics_formats.md` ### 3. Microscopy and Imaging Formats (45+ extensions) Microscopy images, medical imaging, whole slide imaging, and electron microscopy. **File types include:** `.tif`, `.nd2`, `.lif`, `.czi`, `.ims`, `.dcm`, `.nii`, `.mrc`, `.dm3`, `.vsi`, `.svs`, `.ome.tiff`, and more. **Reference file:** `references/microscopy_imaging_formats.md` ### 4. Spectroscopy and Analytical Chemistry Formats (35+ extensions) NMR, mass spectrometry, IR/Raman, UV-Vis, X-ray, chromatography, and other analytical techniques. **File types include:** `.fid`, `.mzML`, `.mzXML`, `.raw`, `.mgf`, `.spc`, `.jdx`, `.xy`, `.cif` (crystallography), `.wdf`, and more. **Reference file:** `references/spectroscopy_analytical_formats.md` ### 5. Proteomics and Metabolomics Formats (30+ extensions) Mass spec proteomics, metabolomics, lipidomics, and multi-omics data. **File types include:** `.mzML`, `.pepXML`, `.protXML`, `.mzid`, `.mzTab`, `.sky`, `.mgf`, `.msp`, `.h5ad`, and more. **Reference file:** `references/proteomics_metabolomics_formats.