Normalize Single Cell Data

The Normalize Single Cell Data tool transforms count data so as to remove the effect of sequencing depth and, optionally, the effect of batch factors. It is recommended to use this tool prior to downstream analysis.

Normalize Single Cell Data can be found in the Toolbox here:

        Gene Expression (Image sc_gene_expression_folder_open_16_n_p) | Cell Preparation (Image sc_cellprep_folder_open_16_n_p) | Normalize Single Cell Data (Image normalize_matrix_16_n_p)

The tool takes at least one Expression Matrix (Image expression_matrix_track_16_n_p) / (Image expr_matrix_spliced_unspliced_16_n_p) as input, and produces a single Expression Matrix (Image expression_matrix_track_16_n_p) / (Image expr_matrix_spliced_unspliced_16_n_p) as output. If multiple Expression Matrixes are provided as input, the single Expression Matrix output will be filtered to only contain those genes that are present in all of the inputs. A report can optionally also be output.

There are three ways of using the Normalize Single Cell Data tool, which differ in how batch correction is performed:



Subsections