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How to create a Seurat object in Excel?
Either a matrix -like object with unnormalized data with cells as columns and features as rows or an Assay -derived object For the initial identity class for each cell, choose this field from the cell’s name. E.g. If your cells are named as BARCODE_CLUSTER_CELLTYPE in the input matrix, set names.field to 3 to set the initial identities to CELLTYPE.
Can you load your own data in Seurat?
As such, here we will give you some code snippets that will allow you to do just that. Remember that Seurat has some specific functions to deal with different scRNA technologies, but let’s say that the only data that you have is a gene expression matrix.
How to convert BC matrix to Seurat object?
I usually import filtered feature bc matrix including barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files to R environment by Read10X function, and convert the data to Seurat object by CreateSeuratObject function. However, I found out that some publicly available processed scRNA-seq data was shared only in the format of counts.csv.gz file.
Can a Seurat object be saved to a h5seurat file?
Saving a Seurat object to an h5Seurat file is a fairly painless process. All assays, dimensional reductions, spatial images, and nearest-neighbor graphs are automatically saved as well as extra metadata such as miscellaneous data, command logs, or cell identity classes from a Seurat object.
How to create a Seurat object with unnorm?
Arguments counts Either a matrix -like object with unnorm project Project name for the Seurat object assay Name of the initial assay names.field For the initial identity class for each names.delim For the initial identity class for each
How to create a Seurat object with barcode cluster?
If your cells are named as BARCODE-CLUSTER-CELLTYPE, set this to “-” to separate the cell name into its component parts for picking the relevant field. Additional cell-level metadata to add to the Seurat object. Should be a data.frame where the rows are cell names and the columns are additional metadata fields.
How to reintroduce excluded features in Seurat?
To reintroduce excluded features, create a new object with a lower cutoff. Include cells where at least this many features are detected. In previous versions (<3.0), this function also accepted a parameter to set the expression threshold for a ‘detected’ feature (gene).