Expression matrix files

Matrix files contain the expression measurements of a study; in RNA-Seq, this would be the expression of your cells. The values are used throughout the study in many visualizations. Although the units of the expression data in a processed matrix file are up to the author of the study, we recommend some variant of log2(TPM +1). You can specify your units in the "Expression axis label" field so that, when viewing expression, the axes are correctly labeled. We also require upload of a raw matrix of measurements (like a count matrix) to encourage data sharing and enable data reuse. Please note, cell names in the matrix file must match cell names in other study files (e.g. metadata or cluster files) to support data visualization.

Accepted formats:

Dense matrix
A tab- or comma-delimited file with columns as cells, rows as features. The first column should be feature names, the first row should be cell names. When defining names, please use alphanumeric characters; underscores are also valid. 

Example dense expression matrix file

Sparse Matrix (aka mtx/feature-barcode matrix)
Sparse matrix data, as generated by 10x Genomics, is a Matrix Market file that contains a sparse matrix in coordinate form accompanied by a barcodes file, corresponding to column indices of the sparse matrix and a feature or genes file, corresponding to row indices of the sparse matrix.

Note: Processed matrix file is required for gene expression visualization.