We will try to provide data in a variety of formats for easy use. Additionally,
the raw data for every study is made available through funding agency repositories
(namely GEO, dbGaP, and/or EGA).
This is the standard output format from the Scanpy analysis
toolkit. These files usually contain raw and normalized expression, gene
and cell annotations like cluster labels and sample metadata, and
dimesnionality reduction coordinates.
No matter the file extension here, these are
rdata files, and
contain (1) log-transformed, normalized expression, (2) a dataframe containing
gene names and symbols, and (3) a dataframe containing t-SNE/UMAP
coordinates and cluster labels.
These are for use in our tool CellView.
These files can be opened using the
Loupe Cell Browser by 10X Genomics. We have modified these files to
contain the same dimensionality reduction (typically labeled
and cluster labels (
Custom Cluser) as used in the
Unmodified lists of marker genes for a set of clusters computed in a one-vs-rest