cbTool
: combine and convert your data¶
The script cbTool
included in the Cell Browser package includes a number of utilties
for combining or converting your data. These different functions and how to use them are
described below.
Combining results¶
Metadata¶
You can use the cbTool metaCat
utility to merge the metadata files from different
sources or pipelines (e.g. cbScanpy
or cbSeurat
) into a single one. A command
to do combine a metadata set of metadata files from Scanpy and Seurat with a separate
one might look like this:
cbTool metaCat myMeta.tsv seuratOut/meta.tsv scanpyOut/meta.tsv ./newMeta.tsv --fixDot
The resulting file will include the columns from all three of the original files
combined into a new metadata file. Note that cbTool metaCat
assumes that the first
column of each file contains the same cell identifier that it can use to join them.
Matrices¶
Similar to metaCat
for combining metadata files, cbTool matCat
can be used to
combine expression matrices from different sources. A command combine the two different
matrixes would look like this:
cbTool matCat mat1.tsv.gz mat2.tsv.gz exprMatrix.tsv.gz
Converting mtx to tsv¶
Using cbTool mtx2tsv
, you can convert your expression matrix in matrix market to tsv format
(with one gene per line and one cell per column):
cbTool mtx2tsv matrix.mtx genes.tsv barcodes.tsv exprMatrix.tsv.gz
Fixing R Seurat output¶
The option --fixDot
for cbTool
will work around R’s strange habit of replacing
special characters in the cell identifiers with “.”. Directories created with the
ExportToCellbrowser()
function from R should not have this problem, but others may.