SPICA

Input formats for dataset projection

Submit one or multiple single-cell samples to the SPICA projection web-app. We support the following formats:

10x MEX format

A compressed folder containing one or multiple folders (one folder for each input sample) in the standard [10x MEX format].

hdf5

A compressed folder containing one or multiple [HDF5 matrices].

raw and raw.log2

A compressed folder containing raw (log-normalized) expression matrices, including barcodes and gene names. For example [GSE86028].

rds

A compressed folder containing one or more Seurat objects in .rds format, one .rds file for each sample. This may be useful if you had already pre-processed your data using Seurat and R.

While the dataset is uploading, select the atlas to use as reference and the dataset format. When data uploading is complete, click on New Project. See the Tutorials for more information on how to prepare and analyze your data.