1. Clone this repo. On your terminal, navigate to a directory of your choosing
cd <dir>
git clone https://github.com/sdarmanis/Neuroendocrine_SCRNAseq.git
2. Download Input files from here and move the .zip file inside the repo directory (which should be called Neuroendocrine_SCRNAseq). Unzip and remove .zip file. Now you should have a folder structure that looks like
/Neuroendocrine_SCRNAseq/. In Neuroendocrine_SCRNAseq you should have: input/ scripts/cd <dir>/Neuroendocrine_SCRNAseq
unzip input.zip
rm input.zip
3. From within Rstudio open /scripts/NE01.Rmd and start from importing data tables and metadata. You can generate the files needed for Scrublet analysis and then switch to the python notebook for running Scrublet. Once finished, switch back to R for importing Scrublet output and filtering doublets.
Note Scrublet doublet analysis for the NE adult data is performed in NE02_Scrublet_raw.Rmd and NE_scrublet_basics.ipynb