Re-organize files into latest file structure

[lcolladotor]

The idea is to update the file structure to reflect https://lcolladotor.github.io/bioc_team_ds/organizing-your-work.html#jhpce-file-organization.

Roche_Habenula

• [x] habenula_*csv -> raw-data/sample_info/bulk/
• [x] prep_manifest.R -> code/01_bulk_speaqeasy/
• [x] count_data -> processed-data/01_bulk_speaqeasy
• [x] qc_data.R -> code/02_bulk_qc/
• [x] qc_plots -> plots/02_bulk_qc
• [x] pc_explore.R -> code/03_bulk_pca/
• [x] pca_plots -> plots/03_bulk_pca
• [x] de_analysis*.R -> code/04_bulk_DE
• [x] genewalk.sh -> code/05_bulk_genewalk/genewalk.sh
• [x] genewalk -> processed-data/05_bulk_genewalk
• [x] Deconvolution -> code/06_deconvolution_trial (move output into plots/06_deconvolution_trial and processed_data/06_deconvolution_trial
• [x] pdfs -> plots/ and maybe re-organized into smaller directories like 04_bulk_DE
• [x] rdas -> processed-data/ and then sub-directories
• [x] tables -> processed-data/ and sub-directories
• [x] power_diff*.R -> code/99_grant_power/

Erik_Habenula

• [x] snRNA-seq/jobSubmit*.sh -> code/07_cellranger/
• [x] snRNA-seq/logs -> code/07_cellranger/logs
• [x] snRNA-seq/Br* -> processed-data/07_cellranger/
• [x] snRNA-seq/20210323_human_hb_neun.R -> code/08_snRNA-seq_Erik/
• [x] snRNA-seq/20210525_human_hb_processing.rda -> processed-data/08_snRNA-seq_Erik/
• [x] snRNA-seq/s3e_hb.rda -> processed-data/08_snRNA-seq_Erik/
• [x] snRNA-seq/human_hb_markers_k10.pdf -> plots/08_snRNA-seq_Erik/

At this point snRNA-seq should be empty and we could delete it.

README

• [x] Create smaller READMEs under plots/* and processed-data/* then move parts of what you have in the current README.md there. Also use bullet points and the single back-tick syntax for differentiating file names from text.

Example:

* `file_01.pdf`: description
* `file_02.pdf`: description

This is how it looks:

• file_01.pdf: description
• file_02.pdf: description

PD For now we aren't going to re-organize /dcs04/lieber/lcolladotor/pilotHb_LIBD001/Visium_Hb since we have to decide with @kmaynard12 whether Visium will be used in this project or not. TBD!

[lcolladotor]

FYI: note that Leo is transferring the data to /dcs04/lieber/lcolladotor/pilotHb_LIBD001/Roche_Habenula right now.

Once all the data is transferred, we could rename the directory as well as this repo. In any case, we need to update the JHPCE location on the main README.md. I would also move it to the end of the README.md since that's internal info that once the repo is public, won't make much sense for others to see at the top. Like:

# Internal

* JHPCE location: `/dcs04/lieber/lcolladotor/pilotHb_LIBD001/Roche_Habenula`