SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
OrthoFinder: accurate gene families made easy! Steve_Kelly Bioinformatics 2 11-20-2018 11:31 AM
Course. Analysis of single cell RNA-seq data.25 February-1 March 2019 in Berlin (Germ Physalia-courses Bioinformatics 0 07-10-2018 01:16 AM
"home-made" Tn5 transposase for single-cell RNA-seq Simone78 Literature Watch 2 08-21-2014 02:38 PM

Reply
 
Thread Tools
Old 09-25-2018, 10:45 AM   #1
jenniferpham
Junior Member
 
Location: San Diego

Join Date: Jun 2018
Posts: 5
Default BioTuring Browser: published single-cell RNA-seq data analysis made easy

Hi everyone,

I am glad to let you know about the release of BioTuring Browser, our dynamic platform that makes access to published single-cell RNA-seq data as easy as surfing a web page.

Since the advent of the single-cell RNA-seq technology, much single-cell data have been generated and made available for the public to access, reanalyze, and facilitate further research. However, single-cell data are pretty huge, requiring powerful computers and command lines to process - that creates a major bottleneck in reproducing a result, or combining datasets from different studies.

With BioTuring Browser, we aim to provide scientists with easy access to published single-cell RNA-seq data. All they need to do is sit down at their laptops, browse a dataset, and land on a 3D visualization of it right away. The ultimate goal is to foster transparency in science and facilitate further research in the single-cell transcriptomic era. Here's a short intro of it: https://www.youtube.com/watch?v=9qCSmPQAUuw

BioTuring Browser comes with numerous options for exploring single-cell data. May I list a few of them:
  • Interactive 3D/2D visualizations of up to 1 million cells on a standard laptop
  • Real-time cell type prediction
  • Batch effect removal (https://www.youtube.com/watch?v=0N7vouZqEoo&t=2s)
  • Differential expression analysis
  • Cell population comparison
  • A curated knowledge base of well-known marker genes from published studies
  • The ability to select and label cell clusters for further annotation
  • Sub-clustering



Future enhancements will include pseudotime trajectory reconstruction, differential expression, and the ability to search for similar single cell populations, and to combine them into the current study.

As a start, BioTuring Browser features nearly 400 publications, including almost all the recent single-cell RNA sequencing datasets and nearly 16,500 samples from bulk RNA sequencing.

With highly optimized algorithms, BioTuring Browser can run on a standard desktop and will be available for Windows, Mac, and Linux.

For now, you can get a beta version at https://bioturing.com

Feel free to raise your questions. If you are interested, please subscribe to be the first to hear about BioTuring Browser official release.
__________________
Jennifer Pham
BioTuring Team
www.bioturing.com
BioVinci: modern data visualizations and analysis for life sciences (https://vinci.bioturing.com)
BioTuring Browser: making access to published single-cell sequencing data as easy as surfing the web (https://bioturing.com/product/bbrowser)
Our blog: https://blog.bioturing.com

Last edited by jenniferpham; 10-18-2018 at 09:46 PM.
jenniferpham is offline   Reply With Quote
Old 09-25-2018, 08:51 PM   #2
jackson48
Junior Member
 
Location: San Francisco

Join Date: Jun 2018
Posts: 2
Default

nice, when is it available?
jackson48 is offline   Reply With Quote
Old 10-01-2018, 04:41 AM   #3
jenniferpham
Junior Member
 
Location: San Diego

Join Date: Jun 2018
Posts: 5
Default

Quote:
Originally Posted by jackson48 View Post
nice, when is it available?
Hi Jackson, the beta version is now available at https://bioturing.com
__________________
Jennifer Pham
BioTuring Team
www.bioturing.com
BioVinci: modern data visualizations and analysis for life sciences (https://vinci.bioturing.com)
BioTuring Browser: making access to published single-cell sequencing data as easy as surfing the web (https://bioturing.com/product/bbrowser)
Our blog: https://blog.bioturing.com
jenniferpham is offline   Reply With Quote
Old 10-05-2018, 03:01 AM   #4
jenniferpham
Junior Member
 
Location: San Diego

Join Date: Jun 2018
Posts: 5
Default

BioTuring Browser was featured on Genomeweb: https://www.genomeweb.com/informatic...a#.W7c2iRP7SnQ
__________________
Jennifer Pham
BioTuring Team
www.bioturing.com
BioVinci: modern data visualizations and analysis for life sciences (https://vinci.bioturing.com)
BioTuring Browser: making access to published single-cell sequencing data as easy as surfing the web (https://bioturing.com/product/bbrowser)
Our blog: https://blog.bioturing.com
jenniferpham is offline   Reply With Quote
Old 10-09-2018, 03:01 AM   #5
jackson48
Junior Member
 
Location: San Francisco

Join Date: Jun 2018
Posts: 2
Default

Quote:
Originally Posted by jenniferpham View Post
Hi Jackson, the beta version is now available at https://bioturing.com
Hello Jennifer, thanks for your reply. I have a couple of questions that might need your help:
- Is it for published data only?
- Do you charge on it?
- What are the system requirements for this tool?
- Could you share when the pseudotime is ready for use?

Thanks,
Jack.
jackson48 is offline   Reply With Quote
Old 10-18-2018, 07:58 PM   #6
jenniferpham
Junior Member
 
Location: San Diego

Join Date: Jun 2018
Posts: 5
Default

Hi Jackson, you can analyze both the published data (free) and private data (charged) in BBrowser. The package can run well on 8GB RAM Mac, Windows, and Linux machines.
We are going through final testing for the pseudotime and will soon bring it out. You can go to bioturing.com/product/bbrowser to subscribe to get updated about it.
__________________
Jennifer Pham
BioTuring Team
www.bioturing.com
BioVinci: modern data visualizations and analysis for life sciences (https://vinci.bioturing.com)
BioTuring Browser: making access to published single-cell sequencing data as easy as surfing the web (https://bioturing.com/product/bbrowser)
Our blog: https://blog.bioturing.com
jenniferpham is offline   Reply With Quote
Old 10-18-2018, 09:44 PM   #7
jenniferpham
Junior Member
 
Location: San Diego

Join Date: Jun 2018
Posts: 5
Default

Batch effect removal and differential expression analysis have been added to BBrowser in the next release: https://www.youtube.com/watch?v=0N7vouZqEoo&t=2s
__________________
Jennifer Pham
BioTuring Team
www.bioturing.com
BioVinci: modern data visualizations and analysis for life sciences (https://vinci.bioturing.com)
BioTuring Browser: making access to published single-cell sequencing data as easy as surfing the web (https://bioturing.com/product/bbrowser)
Our blog: https://blog.bioturing.com
jenniferpham is offline   Reply With Quote
Reply

Tags
bioturingbrowser, single cell, single cell analysis, single cell rnaseq, single-cell sequencing

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 02:53 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO