CINdex: A Bioconductor Package for Analysis of Chromosome Instability in DNA Copy Number Data
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CINdex: A Bioconductor Package for Analysis of Chromosome Instability in DNA Copy Number Data
The CINdex Bioconductor package addresses an important area of high-throughput genomic analysis. It calculates the chromosome instability (CIN) index, a novel measurement that quantitatively characterizes genome-wide copy number alterations (CNAs) as a measure of CIN. The advantage of this package is an ability to compare CIN index values between several groups for patients (case and control gr...
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This document guides the reader through the use of the seqCNA package. The aim of the package is to process high-throughput sequencing copy number data coming from tumoural samples, departing from SAM or BAM aligned reads up to the final stage of calling the copy numbers. It includes, among other features, an integrated summarization method, several filters based on a range of genomic and read-...
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Copy-number-aware differential analysis of quantitative DNA sequencing data.
Developments in microarray and high-throughput sequencing (HTS) technologies have resulted in a rapid expansion of research into epigenomic changes that occur in normal development and in the progression of disease, such as cancer. Not surprisingly, copy number variation (CNV) has a direct effect on HTS read densities and can therefore bias differential detection results. We have developed a fl...
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ژورنال
عنوان ژورنال: Cancer Informatics
سال: 2017
ISSN: 1176-9351,1176-9351
DOI: 10.1177/1176935117746637