SPRING is a tool for uncovering high-dimensional structure in single-cell gene expression data. SPRING takes a (gene X cell) table of expression measurements and outputs a k-nearest-neighbor graph rendered using a force directed layout. Users can overlay prior information, including gene expression values, gene-set scores, cell cluster labels and sample IDs. Users can also upload custom coordinates that have been generated using an outside program such as tSNE.

Basics

Menus

Selections

Dynamics

Subplots

Upload your own data

April 2018: We have made a major update to the SPRING viewer, as well as some minor changes to this upload tool. Please contact Caleb Weinreb (calebsw@gmail.com) or Sam Wolock (swolock@gmail.com) with questions.

Step 1: Load data

Upload a new dataset or load an exisiting one

Expression data
Gene list
Cell groupings
Custom color tracks
Custom coordinates Gene sets

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Submit a text file in the following format (do not include a header)
Files can be compressed in the ".gz" or ".zip" formats.

The following formats are accepted: {.csv, .tsv, .npy (numpy), .npz (scipy sparse), .mtx}.

Download example file

This file should contain a single-cell gene expression matrix. If a csv/tsv file is uploaded, non-numeric columns/rows at the beginning of the file will be skipped.

Choose file

Step 2: Process data

Minimum UMI total (for filtering cells)

Min number of cells with >=3 counts (for filtering genes)

Gene variability percentile (for filtering genes)

Number of PCA dimensions (for building graph)

Number of nearest neighbors (for graph)

Email address

Step 3: Click here to view data

Please send problems or suggestions to

calebsw@gmail.com Klein lab website