AllelicImbalance: an R/ bioconductor package for detecting, managing, and visualizing allele expression imbalance data from RNA sequencing
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- 作者：Jesper R. Gådin ; Ferdinand M. van't Hooft ; Per Eriksson…
- 关键词：Allelic imbalance ; Allele ; specific expression ; RNA sequencing ; Gene expression ; SNP
- 刊名：BMC Bioinformatics
- 出版年：2015
- 出版时间：December 2015
- 年：2015
- 卷：16
- 期：1
- 全文大小：1,534 KB
- 刊物主题：Bioinformatics; Microarrays; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Combinatorial Libraries; Algorithms;
- 出版者：BioMed Central
- ISSN：1471-2105
文摘
Background One aspect in which RNA sequencing is more valuable than microarray-based methods is the ability to examine the allelic imbalance of the expression of a gene. This process is often a complex task that entails quality control, alignment, and the counting of reads over heterozygous single-nucleotide polymorphisms. Allelic imbalance analysis is subject to technical biases, due to differences in the sequences of the measured alleles. Flexible bioinformatics tools are needed to ease the workflow while retaining as much RNA sequencing information as possible throughout the analysis to detect and address the possible biases.