Storage and Curation of data generated from the HMHZ

This repository is for storage, curation and documentation of all relevant data on wild mice capture following laboratory assays including detection of Eimeria, Cryptosporidium, worms, gene expression, etc...

Structure:

data_input

All input data is kept together (can be merged by the identifier) _"MouseID", other columns should not be repeated in input data tables. The columns are documented for the different categories of input data as indicated in the documentation folder.

data_products

Analysis ready datasets to be used (or which have been used) in research projects

R

Code required for data processing and curation

raw2input

Contains code that might be helpful to curate the data before it goes into data_input

input2product

Code producing final data products in data_products

analysis

Contains some old data analysis scripts. PLEASE DON'T use this repository TO TRACK DATA ANALYSIS projects. The data analysis scripts tracks here should be purely for reviewing the correctness of data. The older scripts are left here for inspiration for now. We might remove them.

documentation

Main Documentation file in csv format. New variables should be added continuously.

• Assay: What kind of assay the variable is derived from
• Variable: Name in data tables
• Description: precise description of variable meaning
• Type: Data type (numeric, logical, character)
• Unit: if applicable
• Values: for orientation
• Correction needed: specifies that data in SOTA may need some modification because of comma-errors or specific issues (date unification, different input across the years)
• aka: outdated names

Freezer Samples (-80)

Here you can find the link to all freezer samples. If you take boxes upstairs to the -20 freezer, please adjust the sheet accordingly, so we are always up to date!