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: 6
Default BioTuring Browser: tackle challenges in single-cell RNA-seq data analysis

Hi everyone,

I am glad to let you know about the official release of BioTuring Browser, the platform to resolve major challenges in single-cell RNA-seq data analysis.

With the proliferation of the single-cell RNA-seq data, we are now facing a major bottleneck in data analysis, because such enormous amounts of data require really hard code to process, and a strong computer to visualize thousands to millions of data points (i.e. thousands to millions of cells).

With BioTuring Browser, we aim to make single-cell RNA-seq data analysis extremely easy and compact for every biologist. The package can run well on a standard laptop, show up in an interactive interface that is simple to use, and provide all the state-of-the-art analyses for scRNA-seq data.

Here's to list a few features in BBrowser:
  • 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
  • The ability to select and label cell clusters for further annotation
  • Sub-clustering
  • View 2 genes' expression at the same time
  • View box plots/ violin plots of the expression levels across all the groups

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

Also, BBrowser provides a rich library of scRNA-seq datasets from latest published studies, all processed and ready for visualization and reanalysis. The purpose is to remove any barriers to access valuable published data, and make science completely transparent.



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.

BBrowser is available for Windows, Mac, and Linux 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; 12-12-2018 at 02:51 AM.
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: 6
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: 6
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: 6
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: 6
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
Old 12-12-2018, 03:28 AM   #8
jenniferpham
Junior Member
 
Location: San Diego

Join Date: Jun 2018
Posts: 6
Default

Exploring the single-cell atlas of the maternal-fetal interface https://www.youtube.com/watch?v=YgkzT2fsvk8
__________________
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 05:47 PM.


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