Import Expression Matrix

Several formats can be imported into an Expression Matrix (Image expression_matrix_track_16_n_p) using the following importers:

The importers can be found here:

        Import (Image Next_Folder_16_n_p) | Single Cell Data (Image single_cell_importers_16_n_p) | Import Expression Matrix (Image import_matrix_16_n_p)

Some other commonly encountered formats are specific to a programming language or software package. These can usually be exported from that software package as Loom files. For example, .rds/.Robj formats are from the R programming language and can often be written to Loom using the LoomR package, or methods in the same R package that was used to generate the files.

General options

The following options are common to all expression matrix importers:

Options for importing cell annotations and clusters

AnnData, h5Seurat, Loom, and Parse Bio MTX can contain metadata about cells, and this can be imported as Cell Annotations (Image cell_annotations_16_n_p) or Cell Clusters (Image cell_clusters_16_n_p). These importers share the following options:

Options for importing spliced and unspliced counts

Loom and MEX formats can contain both the total expression, spliced, and unspliced counts. The importers can be configured with which type of data to import and produce either an Expression Matrix (Image expression_matrix_track_16_n_p), or an Expression Matrix with spliced and unspliced counts (Image expr_matrix_spliced_unspliced_16_n_p).



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