SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Gene set enrichment analysis of RNA-Seq data jel4h Bioinformatics 1 06-21-2012 04:25 AM
RNA-Seq: GENE-Counter: A Computational Pipeline for the Analysis of RNA-Seq Data for Newsbot! Literature Watch 0 10-15-2011 03:11 AM
RNA-Seq: Length Bias Correction for RNA-seq Data in Gene Set Analyses. Newsbot! Literature Watch 0 01-22-2011 02:02 AM

Reply
 
Thread Tools
Old 04-15-2013, 04:41 PM   #1
Xi Wang
Senior Member
 
Location: MDC, Berlin, Germany

Join Date: Oct 2009
Posts: 317
Default SeqGSEA: Gene Set Enrichment Analysis of RNA-Seq Data

I am glad to introduce to you guys a new Bioconductor package, SeqGSEA, developed by our group. The detailed description of this package is:

SeqGSEA: Gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. Using negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Statistical significance of each gene set investigated is reached by subject permutation. Based on the permutation, statistical significance regarding to each gene's differential expression and splicing can also be achieved , respectively.

The package can be accessed at the URL:
http://bioconductor.org/packages/rel...l/SeqGSEA.html

Should you have any questions, comments, or suggestions, please feel free to email me at (xi.wang (at) newcastle.edu.au). Thanks.
__________________
Xi Wang
Xi Wang is offline   Reply With Quote
Old 04-23-2013, 11:12 PM   #2
Xi Wang
Senior Member
 
Location: MDC, Berlin, Germany

Join Date: Oct 2009
Posts: 317
Default

Just in case some of you didn't see the original post :-)
__________________
Xi Wang
Xi Wang is offline   Reply With Quote
Old 10-01-2013, 07:15 AM   #3
elgarcia
Junior Member
 
Location: NC, USA

Join Date: Sep 2013
Posts: 1
Default

Xi,

Can SeqGSEA be used with Drosophila data?

I run into a problem with my genesets. I've tried Ensemble gene IDs and gene symbols, but none pass the initial size filter. It gives the following error on GSEnrichAnalyze:

Error: all(i <= size(x)) is not TRUE

Thanks.
elgarcia is offline   Reply With Quote
Old 10-01-2013, 07:44 AM   #4
Xi Wang
Senior Member
 
Location: MDC, Berlin, Germany

Join Date: Oct 2009
Posts: 317
Default

Quote:
Originally Posted by elgarcia View Post
Xi,

Can SeqGSEA be used with Drosophila data?

I run into a problem with my genesets. I've tried Ensemble gene IDs and gene symbols, but none pass the initial size filter. It gives the following error on GSEnrichAnalyze:

Error: all(i <= size(x)) is not TRUE

Thanks.
Hi Can you describe your problem in more details, including information such as how your gene IDs look like and what kind of gene set data you have, and can you send them to me via email: xi.wang@newcastle.edu.au

Thanks
Xi
__________________
Xi Wang
Xi Wang is offline   Reply With Quote
Reply

Tags
gsea, rna-seq, seqgsea

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 01:34 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO