Processing of excel/csv files

Deciding how to deal with csv and excel files used for analysis

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?