Cell Browser best practices

Best Practices

Formatting configuration files

• 80-120 chars per line; use (gqgq in VIM to auto format a paragraph into multiple ~80 char lines
• For special characters, please refer to HTML character encoding: https://ascii.cl/htmlcodes.htm

cellbrowser.conf

Put things into cellbrowser-confs repo Commit cellbrowser/desc.conf files(http://genomewiki.ucsc.edu/genecats/index.php/Wrangling_process#Commit_cellbrowser.2Fdesc.conf_files)

Git add dataset-name

Git commit -m “message”

Git push

Naming datasets

Dataset names should be all lowercase, using 4 words or less with less than 20 characters and separated by hyphens. The names need to be lowercased because the Cell Browser (website) code converts all names lowercase. There are only a few exceptions for early datasets [e.g. https://cells-test.gi.ucsc.edu/?ds=adultPancreas adultPancreas]

Capitalizing UMAP/tSNE/etc

Capitalize "UMAP" and "tSNE"

Remove extra layout coordinates (e.g. PCA or Harmony) because the cbImportTools export all of the possible layouts. The CB can only handle two coordinates and so these layouts often look like a clump of cells. Remove extra layout coordinates (e.g. PCA or Harmony) since cbImport tools only export the first two coordinates

Finding a paper associated with a bioRxiv pub

https://redmine.soe.ucsc.edu/issues/27316#change-267287 Doi.org *remove \ from DOI

Providing the Unit for datasets

unit="" Ask the author Search Seurat data slot normalized

desc.conf

Paper URL:

paper_url = “url to paper last name et al. Journal. Year.” Journal short name from pubmed

For the description page => first word capitalized, rest is lowercase

Labels for various desc.conf settings => paper URL or website

GSE, Bioproject, SRA accessions, PMID, just put the number, no author info: