Re-organize code so the whole snRNA-seq analysis is reproducible

[lcolladotor]

• [x] Move https://github.com/LieberInstitute/Habenula_Bulk/blob/master/code/08_snRNA-seq_Erik/20220228_human_hb_neun.R#L10-L109 to it's own script (likely with a 01_ prefix) at 09_snRNA-seq_re-processed
• [x] Change the SCE object name to something different to what Erik used. To make it easier for us to know which one we are referring to, instead of re-using s3e.hb. Choose something easy to type ^^. Aka, you won't need https://github.com/LieberInstitute/Habenula_Bulk/blob/master/code/09_snRNA-seq_re-processed/01_qc.R#L42 anymore.
• [x] Save the emptyDrops() output into it's own Rdata file https://github.com/LieberInstitute/Habenula_Bulk/blob/master/code/08_snRNA-seq_Erik/20220228_human_hb_neun.R#L108
• [x] Before saving the SCE object, add the gene information using the code from https://github.com/LieberInstitute/spatialLIBD/blob/master/R/read10xVisiumWrapper.R#L86-L113 where reference_gtf https://github.com/LieberInstitute/spatialLIBD/blob/master/R/read10xVisiumWrapper.R#L88 can be /dcs04/lieber/lcolladotor/annotationFiles_LIBD001/10x/refdata-gex-GRCh38-2020-A/enes/genes.gtf taken from http://research.libd.org/spatialLIBD/articles/TenX_data_download.html#from-10x or you could use the exact same one Erik used at https://github.com/LieberInstitute/Habenula_Bulk/blob/master/code/08_snRNA-seq_Erik/20210323_human_hb_neun.R#L197 which is /dcl01/ajaffe/data/lab/singleCell/cellranger_reference/refdata-gex-GRCh38-2020-A/genes/genes.gtf. Both files are in reality identical and I would encourage that you use the one from dcs04.
• [x] Also before saving your initial SCE, import the results from Erik, so we'll have them from the beginning. That's from https://github.com/LieberInstitute/Habenula_Bulk/blob/master/code/09_snRNA-seq_re-processed/01_qc.R#L46-L53. Note that we'll need to this this in the reverse order, so change the order of the inputs at match() https://github.com/LieberInstitute/Habenula_Bulk/blob/master/code/09_snRNA-seq_re-processed/01_qc.R#L49 and how things are assigned at https://github.com/LieberInstitute/Habenula_Bulk/blob/master/code/09_snRNA-seq_re-processed/01_qc.R#L50-L53.
• [x] Also keep Erik's cell type labels (s3e.hb$cellType) as sce$cellType_Erik or something like that (change sce for whatever name you used earlier).
• [x] You can likely delete https://github.com/LieberInstitute/Habenula_Bulk/blob/master/code/08_snRNA-seq_Erik/20220228_human_hb_neun.R to avoid confusion.
• [x] You could then use sgejobs::job_single() to add a shell script if you want to be able to qsub this new R script. You can then have a single shell script for re-running everything if needed, like https://github.com/LieberInstitute/Visium_IF_AD/blob/master/code/run_all_post_spaceranger.sh for example.
• [x] Rename https://github.com/LieberInstitute/Habenula_Bulk/blob/master/code/09_snRNA-seq_re-processed/01_qc.R to be something like 02_qc.R.
• [x] Load your own data (post-emptyDrops()) instead of Erik's at https://github.com/LieberInstitute/Habenula_Bulk/blob/master/code/09_snRNA-seq_re-processed/01_qc.R#L7.