Cell-type annotations are frequently excluded from public single cell
datasets. This hinders single cell sequencing analysis reproducibility
and accessibility. To better describe the issue, we monitor GEO entries
monthly (currently set to auto-update at 1AM UTC, 1st of the month), and
programmatically determine the fraction of entries with (potentially,
likely overestimated) usable cell metadata. Descriptions of the issue
and suggestions (in short: PLEASE PLEASE deposit some metadata at cell
level for scRNA-seq data) are now published on PLoS
Biology.
Supplemental data files related to the manuscript are located in the
inst/manuscript/ directory.
Additional thoughtful guidelines for organizing scRNA-seq sample and cell metadata are discussed here by Füllgrabe et al.
The latest archive of GEO scRNA-seq records with other associated data
can be directly downloaded here
current_geo.rds.
GEO filtering, preview first lines of text files, and content of .tar,
and spot check feedback can be accessed from last tab on the clustifyr
web
app.
As of the initial presentation of this issue (10–17–2020), the number is a frustratingly low 0.122.
Current fraction in GEO with metadata: 0.1836735. In comparison, for ArrayExpress 10x datasets, the fraction is 0.1463415).
Number of depositions with updated metadata records since description of the issue here: 0.
Please also see full report page.
