Dataset metadata

Regina H. Reynolds

UCL
regina.reynolds.16@ucl.ac.uk

3 February 2023

Descriptions for metadata columns

Dataset metadata

Generation of specificity matrices/dataframes

• The majority of specificity matrices have been downloaded from external sources (primarily Skene 2018; with specificity matrices made available in the associated GitHub repo).
• A few specificity matrices have been specifically generated within the MarkerGene package. These can be divided into their compatibility with EWCE versions:
  • Compatible with the defunct EWCE v1.3.0 available on Bioconductor v3.5
    • Zeisel et al. 2018 (see: Zeisel2018_CNSClusters_FormattingDataForEWCE.R)
    • Allen Brain Atlas 2018 (only MTG).
      • Downloaded from AIBS.
      • Used gene-level (exonic) read count values.
      • For code on how this was generated, please refer to: AIBS2018_GeneratingSImatrix.R.
    • Agarwal 2020.
      • Data downloaded from GEO.
      • For code on how this was generated, please refer to: Agarwal2020_GeneratingSImatrix.R
  • Compatible with the new EWCE that is available in Bioconductor>=3.14
    • Allen Brain Atlas 2018 (multiple cortical areas)
      • Downloaded from AIBS.
      • Used gene-level (exonic) read count values.
      • For code on how this was generated, please refer to: AIBS2019_GeneratingSImatrix.R and AIBS2019_ctd_generation_description.html
    • Zeisel et al. 2018, downloaded from http://mousebrain.org/adolescent/downloads.html
      • For code on how this was generated, please refer to: Zeisel2018_generate_new_ctd.R
• Finally, a specificity dataframe was generated within the MarkerGene package for GTEx v8.
  • This was generated by modifying code from the article, Bryois 2020, which was made available here: https://github.com/jbryois/scRNA_disease/blob/master/Code_Paper/Code_GTEx/get_GTEx_input.md.
  • The primary modification was to include all genes, including non-protein-coding genes, which were previously excluded.
  • For all details on the generation of this specificity dataframe, please refer to: GTEx_v8_specificity.html.