Scripts for biological data analysis
Scripts I've written that were not large enough projects to warrant their own repository. Many of these are dataset and project specific. This is an incomplete history of scripts written and used over the years and will be updated as I find old scripts or create new ones. If you look through them, it sort of represents my progress in learning to write better code, so there's a range of skill level represented here, especially as a self-taught programmer from a more scientific background. Sometimes I go back and update the scripts as well, especially if I start needing to repeat analyses.
Note: Anything with a date in the name is a specific analysis that is more of a history of commands used to perform that analysis and is less likely to be reused.
Folders
This is organized into folders based on broader categories for the type of data analysis or if it was a short, individual project. Here is the basic breakdown:
- lab_assays: Data analysis scripts for various wet lab experiments I did
- next_gen_sequencing: Data analysis scripts & short projects for various NGS data sets, usually mRNA-seq and smRNA-seq. Some for taking raw sequencing data to counts tables and further exploratory analysis and plotting.
- microarray: Data analysis of microarray datasets
- imaging: Imaging data analysis
- misc: everything else