SeqCNA: an R package for DNA copy number analysis in cancer using high-throughput sequencing.

ABSTRACT:

Background

Deviations in the amount of genomic content that arise during tumorigenesis, called copy number alterations, are structural rearrangements that can critically affect gene expression patterns. Additionally, copy number alteration profiles allow insight into cancer discrimination, progression and complexity. On data obtained from high-throughput sequencing, improving quality through GC bias correction and keeping false positives to a minimum help build reliable copy number alteration profiles.

Results

We introduce seqCNA, a parallelized R package for an integral copy number analysis of high-throughput sequencing cancer data. The package includes novel methodology on (i) filtering, reducing false positives, and (ii) GC content correction, improving copy number profil

SUBMITTER: Mosen-Ansorena D 

PROVIDER: S-EPMC4022175 | biostudies-literature | 2014 Mar

REPOSITORIES: biostudies-literature