shRNA-seq data analysis with edgeR
نویسندگان
چکیده
منابع مشابه
shRNA-seq data analysis with edgeR
Pooled short hairpin RNA sequencing (shRNA-seq) screens are becoming increasingly popular in functional genomics research, and there is a need to establish optimal analysis tools to handle such data. Our open-source shRNA processing pipeline in edgeR provides a complete analysis solution for shRNA-seq screen data, that begins with the raw sequence reads and ends with a ranked lists of candidate...
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This article reviews the statistical theory underlying the edgeR software package for differential expression of RNA-seq data. Negative binomial models are used to capture the quadratic mean-variance relationship that can be observed in RNA-seq data. Conditional likelihood methods are used to avoid bias when estimating the level of variation. Empirical Bayes methods are used to allow gene-speci...
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BACKGROUND Several R packages exist for the detection of differentially expressed genes from RNA-Seq data. The analysis process includes three main steps, namely normalization, dispersion estimation and test for differential expression. Quality control steps along this process are recommended but not mandatory, and failing to check the characteristics of the dataset may lead to spurious results...
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ژورنال
عنوان ژورنال: F1000Research
سال: 2014
ISSN: 2046-1402
DOI: 10.12688/f1000research.3928.1