What
alona
is
alona is a web-based bioinformatics service
designed to analyze single cell RNA sequencing (scRNA-seq)
data. This service performs processing, analysis and
visualization using some of the most popular scRNA-seq
algorithms. Cells are annotated into cell types using
marker genes from PanglaoDB. Instead of
using the default marker genes, the user can also provide
such a list. Processed data can be explored from an
intuitive web interface based on JavaScript.
An example of scRNA-seq data from the mouse brain. See below for more examples.
The service is free and it is provided by the Integrated Cardio Metabolic Centre at the Karolinska Institutet .
alona is based on the adobo
Python package
How to cite
O. Franzén & J. Björkegren, alona: a web server for single cell RNA-seq analysis, Bioinformatics (2020), doi:10.1093/bioinformatics/btaa269
How it works
The flowchart to the left illustrates the basic steps
in the analysis. The boxes in yellow illustrate steps
performed by
alona.
A gene expression from a scRNA-seq experiment is accepted as input. Data should have been mapped and reads counted using external software.
The uploaded data can come from any single cell protocol or platform.
The analysis usually completes within 10 to 15 minutes on a dataset consisting of 5000 cells. An e-mail can be sent as a reminder.
alona generates an archive of files in
tar.gz format, containing analysis results and plots.
How to prepare your data
Only a gene expression matrix is needed with genes as rows and cells as columns. Single cell gene expression matrices are often large because thousands of cells are usually sampled. The matrix is either a plain text file, having any arbitrary filename, and it must be compressed using zip, gzip, bzip2 or xz. The correct filename extension must be used for the corresponding compression (i.e. zip for zip, gz for gzip, bz2 for bzip2, and xz for xz).
Uploaded data must not be normalized; i.e., measurements should be raw read counts.
File name: The file name is only allowed to contain the following types of characters: letters (a-z), numbers (0-9), dashes (-), underscores (_), white spaces, and dots (.).
Detailed description on data preparation from sequences
alona
assumes that you have already performed
basic data processing (alignments, read counting, etc). See
here
for
our
guide on how to preparing a dataset for analysis with
alona.
Supported data formats
- A compressed plain text gene expression matrix in one of the following formats:
- gzip
- bzip2
- zip
- xz
- Matrix market (format described here). This is a popular sparse format used in NCBI's GEO. If this format is chosen, there should be three gzip-compressed files loaded in a single tar.gz archive and the files must have exactly these names: matrix.mtx.gz, barcodes.tsv.gz and genes.tsv.gz
Privacy notice
When your data are uploaded, a cookie is stored in your browser session and it identifies your session. When your browser cache is cleared, you will not be able to see your data any further; as an optional reminder, an email can be sent when data analysis has completed. In the future we might limit how long time data are stored before being automatically deleted. While the "dashboard" is private and specific to your session, the web browser interface to your processed data is public and not protected by login; that means that anyone that knows the full URL to your dataset can view it. An optional password can be set when uploading data to provide additional security.
Standalone version
As mentioned above, this web server is based on adobo — a Python package for single cell RNA-seq analysis. See github.com/oscar-franzen/adobo. The Python code for the performed analysis is included in the attached archive after alona has finished running, and the template can be downloaded here.
Statistics
In average, a dataset runs for 16 minutes.
Current system status
Queued datasets: 878 Running datasets: 0