This is a repository specifically for lakshmi and manisha to store their codes. The codebase will have a specific set of guidelines for the code files management. These will be updated once they have been discussed.
- The major chunks of the codebase are to be devided into separate rmd file.
- The functions that are to be used by more than 1 rmd file are to be put in R folder and sourced in each rmd.
- The plots are to be output in each rmd subfolder in the plots folder. (Though I do not like this paradigm because I am a fan of knitting the rmd file, so that the report is generated, and forwarding the philosophy of the literate programming).
- The intermediate outputs of each rmd that will be used as input by other rmd should be placed in outputs folder.
- The codes should be able to process the raw data as an output from CellProfiler. There should be serial rmd files if need be numbered.
This space will grow.