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 by LanaGarmireGroup, Xun Zhu

Suggested by: Avital Cher


Granatum is a graphical single-cell RNA-seq (scRNA-seq)
analysis pipeline for genomics scientists. The pipeline will graphically guide you through the analysis of scRNA-seq data, starting from expression and metadata tables. It uses a comprehensive set of modules for quality control / normalization, clustering, differential gene expression / enrichment analysis, protein network interaction visualization, and cell pseudo-time pathway construction.


Ask a question or post a review

Is there an easier way to use Granatum? Oval 17

The idea is cool, but the installation process appears to be very long, requires to install VirtualBox etc.. I would love to see this run on some dedicated server

upvotecomment_icon_normal 9 upvotes 6 comments Reply
Posted: 1 year ago

Thomas Wolfgruber

Bioinformatician at University of Hawaii

Thank you for your feedback. I agree that relative to accessing an online server the installation is long. We are looking into getting it online. In the meantime, hopefully you will find that the process is relatively straightforward: 1) install VirtualBox, 2) download the Granatum file, 3) import the file into VirtualBox, and 4) run the file.

upvotecomment_icon_normal 4 upvotes Reply
Posted: 1 year ago


Principal Investigator (PI) at University of Hawaii at Manoa

Hi Marie, thanks for your feed back. We have recently opened Granatum online and you can access it via the following URL: http://garmiregroup.org/granatum/app. No installation is required.

upvotecomment_icon_normal 2 upvotes Reply
Posted: 1 year ago

Wow, that's amazing! thanks for creating this website & informing me.. will try it out!

BTW- does it make sense to load also data collected from multiple wells, where each had about 500cells that were lysed and sequenced ? (of course these are not actually single cells, but small populations)

upvotecomment_icon_normal 2 upvotes Reply
Posted: 1 year ago


Principal Investigator (PI) at University of Hawaii at Manoa

Hi Marie, we are glad that you like it!

It does. Granatum supports uploading multiple datasets, and it even guides you in removing the batch effects if you would like to. The only concern at the moment is that currently (due to limited funding) we only have 8GB RAM available on the public server, which means that large datasets (thousands of cells or more) might take really long time (up to several hours) to finish for some of the key steps. And to avoid the possibility of one user occupying the entire server, the long running processes are subject to termination.

You may try using a random down-sampling of cells (samples), and try raising the threshold of gene filtering to reduce the dataset size.

If you have trouble using Granatum for a particular dataset, feel free to let us know. We may be able to run your data through a dedicated higher capacity server.

You can reach us at:

Principal Investigator: Lana Garmire (LGarmire@cc.hawaii.edu)
Head Developer: Xun Zhu (zhu2@hawaii.edu)

Looking forward to hear from you.



upvotecomment_icon_normal 3 upvotes Reply
Posted: 1 year ago

Hello again,

Just two quick suggestions:
1. Better define the input file requirements (no repeating rows, only integers), spent some time figuring this out (despite the example files)
2. My session was stopped a few times, I only have 48 samples so maybe there is a load on the server. Maybe have add some resource-status indicator..


upvotecomment_icon_normal 1 upvotes Reply
Posted: 1 year ago
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Genomics RNA-Seq

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