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


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.


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.