> For the complete documentation index, see [llms.txt](https://notes123.vladimir-vinarsky.me/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://notes123.vladimir-vinarsky.me/processing-of-excel-csv-files.md).

# Processing of excel/csv files

## What are the files?

* Cell-Profiler output
* Sarcomere App output
* ImageJ measurements
* Sota tool and other tools
* Ilastik output
* One step excel files output
* RNA-seq output

## Use cases

### 1. Stacking of  content of files on top of each other

### 2. Summary statistics for a group defined in column

### 3. Get unique values "levels" from a specified column(s)

### 4. Split one file into multiple based on value in a column "level"

### 5. Load xlsx file, process, save as another list in the file

### 6. Generate a table in word sorted according to specified column

### 7. Generate a report of what was done 

## Why not to do it in R?

* Need to open R studio, takes long to open, requires updates all the time
* takes time to look at different csvs in RStudio
* Do not know how to operate with excel files
* it is difficult to specify the files I want to operate on (globbing in command line is much more easy)
* I do not know how to use the Rscripts from the command line and supply arguments, i do know how to do it in bash

## Why do it in R ?

* I can manipulate the values  (addition/substraction etc)
* I can do statistics (t-tests etc.)
* I can plot
* R community is bigger, easier to share and get recognition
* can make it into a web-app

## How will I share it?