Paper Info
Title
ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets.
Abstract
1RNA sequencing is a flexible and powerful new approach for measuring gene, exon, or isoform expression. To maximize the utility of RNA sequencing data, new statistical methods are needed for clustering, differential expression, and other analyses. A major barrier to the development of new statistical methods is the lack of RNA sequencing datasets that can be easily obtained and analyzed in common statistical software packages such as R. To speed up the development process, we have created a resource of analysis-ready RNA-sequencing datasets. 2ReCount is an online resource of RNA-seq gene count tables and auxilliary data. Tables were built from raw RNA sequencing data from 18 different published studies comprising 475 samples and over 8 billion reads. Using the Myrna package, reads were aligned, overlapped with gene models and tabulated into gene-by-sample count tables that are ready for statistical analysis. Count tables and phenotype data were combined into Bioconductor ExpressionSet objects for ease of analysis. ReCount also contains the Myrna manifest files and R source code used to process the samples, allowing statistical and computational scientists to consider alternative parameter values. 3By combining datasets from many studies and providing data that has already been processed from. fastq format into ready-to-use. RData and. txt files, ReCount facilitates analysis and methods development for RNA-seq count data. We anticipate that ReCount will also be useful for investigators who wish to consider cross-study comparisons and alternative normalization strategies for RNA-seq.
Year
DOI
Venue
2011
10.1186/1471-2105-12-449
BMC Bioinformatics
Keywords
DocType
Volume
microarrays,algorithms,bioinformatics
Journal
12
Issue
ISSN
Citations 
1
1471-2105
37
PageRank 
References 
Authors
2.00
4
3
Name
Order
Citations
PageRank
Alyssa C. Frazee1372.00
Ben Langmead2516.94
Jeffrey T. Leek314813.79