ShinyCNV: a Shiny/R application to view and annotate DNA copy number variations.
Bioinformatics
; 35(1): 126-129, 2019 01 01.
Article
em En
| MEDLINE
| ID: mdl-30561549
ABSTRACT
Motivation Single nucleotide polymorphism (SNP) array is the most widely used platform to assess somatic copy number variations (CNVs) in cancer studies. Many SNP data-based CNV callers are available, however, the false positive rates from automated calling are commonly high, and reported breakpoints can be inaccurate. Manual review for each reported CNV by visualizing the SNP data is important, but is challenging for users lacking computational experience. To address this, we present a Shiny/R application ShinyCNV, an interactive graphical user interface to view and annotate CNVs. Results:
With this application, normalized SNP data, which includes log R ratio (LRR) and B allele frequency, can be plotted against the reported CNVs, and users can visually check the reliability of CNVs per se or adjust the incorrectly assigned breakpoints. Further, the interactive LRR spectrum panel within ShinyCNV can facilitate the process to identify commonly affected CNV regions from a group of samples, and to visually check if important focal gains/losses are missing from reported CNVs. ShinyCNV is designed to be intuitive for cancer researchers and can be easily installed for either personal use or deployed on servers to provide online service. Availability and implementation ShinyCNV and the tutorial are freely available from https//github.com/gzhmat/ShinyCNV. Supplementary information Supplementary data are available at Bioinformatics online.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Software
/
Variações do Número de Cópias de DNA
/
Anotação de Sequência Molecular
/
Neoplasias
Tipo de estudo:
Prognostic_studies
Limite:
Humans
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2019
Tipo de documento:
Article
País de afiliação:
Estados Unidos