UMCG-Microbiome

UMCG Microbiome does simple analyzes and graphs of metagenomical data and bacterial pathway data.

Content:

1. BiomTable_class: reading and parsing csv metaphlan

2. Data_chart: pie chart and bar chart of data groups

3. Diversity_class: calculating shannon, simpson and jaccard index from abundance

4. Box_plot: draws a box plot for a set of metaphlan data

5. PathwayTable_class: reading and filtered pathway abundance file

6. Test_script

7. Examples and database folder that can be used to try out the code

Instructions

For analyzes of metagenomical data BiomTable_class opens Metaphlan files and is used in other scripts. Download this first. To use other scripts download it and get an appropriate example file. PathwayTable_class is only script that does an analyzes of bacterial pathway data.

To test out all scripts, open Test_script, and uncomment testing functions to test out scripts.