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ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets
Alyssa C Frazee1, Ben Langmead, Jeffrey T Leek
1Department of Biostatistics, The Johns Hopkins University Bloomberg School of Public Health, 615 North Wolfe Street, Baltimore, MD 21205, USA.
BMC Bioinformatics
|November 18, 2011
Summary
ReCount provides analysis-ready RNA sequencing datasets, overcoming a major barrier to developing new statistical methods for gene expression analysis. This resource facilitates RNA-seq data exploration and computational tool development.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- RNA sequencing (RNA-seq) is a powerful tool for measuring gene expression.
- Developing new statistical methods for RNA-seq analysis is hindered by data accessibility.
- Analysis-ready datasets are needed to accelerate the development of RNA-seq statistical methods.
Purpose of the Study:
- To create a centralized, accessible resource of RNA-seq gene count data.
- To facilitate the development and application of novel statistical methods for RNA-seq analysis.
- To support cross-study comparisons and alternative normalization strategy investigations.
Main Methods:
- Compiled raw RNA-seq data from 18 published studies (475 samples, >8 billion reads).
- Utilized the Myrna package for read alignment, gene model overlap, and count tabulation.
- Integrated gene-by-sample count tables and phenotype data into Bioconductor ExpressionSet objects.
Main Results:
- Developed ReCount, an online resource of analysis-ready RNA-seq gene count tables.
- Provided processed data in RData and txt formats, ready for statistical analysis.
- Included Myrna manifest files and R source code for transparency and reproducibility.
Conclusions:
- ReCount significantly facilitates RNA-seq data analysis and methods development.
- The resource enables researchers to perform cross-study comparisons and explore normalization strategies.
- ReCount addresses the need for readily available, processed RNA-seq datasets in the scientific community.
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