README.md

# Shiny_Fluxer

## highlights

- loading preferences works again
- multiple bar plots all exported in one pdf


*you need to update your tidyverse packages*

New Shiny Flux tool for 13C tracers

## Example files

In directory `Input`; an example for the old and the new input format

## Input

Reads both old and new format

- Old format: reads only `BIO` and `MEASUREMENT` sheets
- New format: `SAMPLE` and `MEASUREMENT` sheets

### SAMPLE (previously BIO)

- `SAMPLE_ID` (`BIO_SAMPLE_ID`)
- optional columns that will be created with default values if absent: 
a. `INJECTION\_VOLUME`
b. `RUN\_ORDER`
- Any number of other columns. They will be used as design factors if
a. They do not contain missing values
b. They have at least two levels
c. They do not only contain unique values

### MEASUREMENT

Exactly three columns are parsed

- `SAMPLE\_ID`
- `FEATURE\_ID`
- `PEAK\_AREA`

### FEATURE\_ID

This replaces `COMPOUND\_ID`. The syntax will be described in detail elsewhere. 

## Processing

The IsoCorrectoR package is immediately called to correct for natural abundance 13C.

## To do
- unify remove variables
- pls
- hclust

## Clean up

- is server_init/0002_wipe...R still required?_