Here we present the methods to test for differential expression analysis in RNAseq and proteomics that was reported in "Distinct sub-cellular autophagy impairments occur independently of protein aggregation in aged induced neurons from patients with Huntington’s disease" (Pircs, et al., not yet published).

We have organized the papers results into eight sections, each of them with their corresponding R script (named as [number of step]_[description]). Please note that these scripts are dependent to one another, so they save their environment and the next one loads the previous one, they are described (in order) below:

An perhaps easier way of running and visualizing the results is checking the R markdown (just one), which combines all the scripts and have some more documentation about the code.