Demo Data

Example datasets for testing MKrep analysis tools

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Available Demo Datasets

Download these example datasets to test the analysis tools. All files are in the required CSV format with binary (0/1) values.

MIC.csv

Minimum Inhibitory Concentration data for various antibiotics

  • Rows: Bacterial strains (with Strain_ID)
  • Columns: Antibiotics (binary: 0 = susceptible, 1 = resistant)
  • Size: ~3KB, 50+ strains, 15+ antibiotics
Download MIC.csv

AMR_genes.csv

Antimicrobial resistance genes presence/absence matrix

  • Rows: Bacterial strains (with Strain_ID)
  • Columns: AMR genes (binary: 0 = absent, 1 = present)
  • Size: ~5KB, 50+ strains, 30+ genes
Download AMR_genes.csv

Virulence.csv

Virulence factors presence/absence data

  • Rows: Bacterial strains (with Strain_ID)
  • Columns: Virulence factors (binary: 0 = absent, 1 = present)
  • Size: ~20KB, 50+ strains, 100+ factors
Download Virulence.csv

MLST.csv

Multi-Locus Sequence Typing data

  • Rows: Bacterial strains (with Strain_ID)
  • Columns: MLST alleles and sequence types
  • Size: ~2KB, 50+ strains
Download MLST.csv

Serotype.csv

Serological typing information

  • Rows: Bacterial strains (with Strain_ID)
  • Columns: Serotype classifications
Download Serotype.csv

Plasmid.csv

Plasmid presence/absence profiles

  • Rows: Bacterial strains (with Strain_ID)
  • Columns: Plasmid types (binary: 0 = absent, 1 = present)
Download Plasmid.csv

MGE.csv

Mobile Genetic Elements data

  • Rows: Bacterial strains (with Strain_ID)
  • Columns: MGE types (binary: 0 = absent, 1 = present)
Download MGE.csv

Snp_tree.newick

Phylogenetic tree in Newick format (for phylogenetic analyses)

  • Format: Newick tree format
  • Tips: Same strains as in CSV files
Download Snp_tree.newick

Complete Dataset Bundle

Download all files at once from the GitHub repository:

Download Complete Repository (ZIP)

Contains all source code, documentation, and example data

Data Format Requirements

Important Format Guidelines
  • First Column: Must be named "Strain_ID" (case-sensitive)
  • Binary Values: Use only 0 (absence) and 1 (presence)
  • No Missing Values: All cells must contain 0 or 1
  • CSV Format: Comma-separated values
  • Unique IDs: Each Strain_ID must be unique

Example Format:

Strain_ID,Gene1,Gene2,Gene3
Strain001,1,0,1
Strain002,0,1,1
Strain003,1,1,0

Using Demo Data

In Google Colab:

  1. Open a Colab notebook from the main page
  2. When prompted, upload the demo CSV files you downloaded
  3. Run the analysis
  4. Download results

Local Installation:

  1. Clone the repository: git clone https://github.com/MK-vet/MKrep.git
  2. Demo files are already included in the repository
  3. Run any analysis script directly

Need Help?

For more information about data preparation and formatting: