wladstroukov / rnaseq-oxldl-macrophages Goto Github PK
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License: GNU General Public License v3.0
Analysis of the of effect of oxidized LDL on macrophages using RNA sequencing
License: GNU General Public License v3.0
Due to the way the Rosalind HPC environment is set up the data cannot be kept in the same repository as the analysis scripts. The data is stored in the /scratch partition of the Rosalind HPC. Hard coding the file paths makes it more difficult to reproduce the pipeline on a different environment (without changing the scripts). Find a work around to avoid hard coded filepaths in the script. One way could be a separate text file that contains the filepaths stored in variable and is loaded into the script. (It would be easier to change the paths in the separate file than adjusting all the scripts.)
Update MA plot function so that genes without adjusted p value will be included in the plot by addition of a conditional so that genes with NA are plotted in light gray.
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