genBaRcode - a comprehensive R package for genetic barcode analysis

Lars Thielecke; Kerstin Cornils; Ingmar Glauche

doi:10.1093/bioinformatics/btz872

genBaRcode - a comprehensive R package for genetic barcode analysis

Standard

genBaRcode - a comprehensive R package for genetic barcode analysis. / Thielecke, Lars; Cornils, Kerstin; Glauche, Ingmar.

In: BIOINFORMATICS, Vol. 36, No. 7, 01.04.2020, p. 2189-2194.

Research output: SCORING: Contribution to journal › SCORING: Journal article › Research › peer-review

Harvard

Thielecke, L, Cornils, K & Glauche, I 2020, 'genBaRcode - a comprehensive R package for genetic barcode analysis', BIOINFORMATICS, vol. 36, no. 7, pp. 2189-2194. https://doi.org/10.1093/bioinformatics/btz872

APA

Thielecke, L., Cornils, K., & Glauche, I. (2020). genBaRcode - a comprehensive R package for genetic barcode analysis. BIOINFORMATICS, 36(7), 2189-2194. https://doi.org/10.1093/bioinformatics/btz872

Vancouver

Thielecke L, Cornils K, Glauche I. genBaRcode - a comprehensive R package for genetic barcode analysis. BIOINFORMATICS. 2020 Apr 1;36(7):2189-2194. https://doi.org/10.1093/bioinformatics/btz872

Bibtex

@article{4b14906dc878413da8dcb01babec70c4,

title = "genBaRcode - a comprehensive R package for genetic barcode analysis",

abstract = "MOTIVATION: Genetic barcodes have been established as an efficient method to trace clonal progeny of uniquely labeled cells by introducing artificial genetic sequences into the corresponding genomes. The assessment of those sequences relies on next generation sequencing and the subsequent analysis aiming to identify sequences of interest and correctly quantifying their abundance.RESULTS: We developed the genBaRcode package as a toolbox combining the flexibility of digesting next generation sequencing reads with or without a sophisticated barcode structure, with a variety of error-correction approaches and the availability of several types of visualization routines. Furthermore, a graphical user interface was incorporated to allow also less experienced R users package-based analyses. Finally, the provided tool is intended to bridge the gap between generating and analyzing barcode data and thereby supporting the establishment of standardized and reproducible analysis strategies.AVAILABILITY AND IMPLEMENTATION: The genBaRcode package is available at CRAN (https://cran.r-project.org/package=genBaRcode).",

author = "Lars Thielecke and Kerstin Cornils and Ingmar Glauche",

year = "2020",

month = apr,

day = "1",

doi = "10.1093/bioinformatics/btz872",

language = "English",

volume = "36",

pages = "2189--2194",

journal = "BIOINFORMATICS",

issn = "1367-4803",

publisher = "Oxford University Press",

number = "7",

}

RIS

TY - JOUR

T1 - genBaRcode - a comprehensive R package for genetic barcode analysis

AU - Thielecke, Lars

AU - Cornils, Kerstin

AU - Glauche, Ingmar

PY - 2020/4/1

Y1 - 2020/4/1

N2 - MOTIVATION: Genetic barcodes have been established as an efficient method to trace clonal progeny of uniquely labeled cells by introducing artificial genetic sequences into the corresponding genomes. The assessment of those sequences relies on next generation sequencing and the subsequent analysis aiming to identify sequences of interest and correctly quantifying their abundance.RESULTS: We developed the genBaRcode package as a toolbox combining the flexibility of digesting next generation sequencing reads with or without a sophisticated barcode structure, with a variety of error-correction approaches and the availability of several types of visualization routines. Furthermore, a graphical user interface was incorporated to allow also less experienced R users package-based analyses. Finally, the provided tool is intended to bridge the gap between generating and analyzing barcode data and thereby supporting the establishment of standardized and reproducible analysis strategies.AVAILABILITY AND IMPLEMENTATION: The genBaRcode package is available at CRAN (https://cran.r-project.org/package=genBaRcode).

AB - MOTIVATION: Genetic barcodes have been established as an efficient method to trace clonal progeny of uniquely labeled cells by introducing artificial genetic sequences into the corresponding genomes. The assessment of those sequences relies on next generation sequencing and the subsequent analysis aiming to identify sequences of interest and correctly quantifying their abundance.RESULTS: We developed the genBaRcode package as a toolbox combining the flexibility of digesting next generation sequencing reads with or without a sophisticated barcode structure, with a variety of error-correction approaches and the availability of several types of visualization routines. Furthermore, a graphical user interface was incorporated to allow also less experienced R users package-based analyses. Finally, the provided tool is intended to bridge the gap between generating and analyzing barcode data and thereby supporting the establishment of standardized and reproducible analysis strategies.AVAILABILITY AND IMPLEMENTATION: The genBaRcode package is available at CRAN (https://cran.r-project.org/package=genBaRcode).

U2 - 10.1093/bioinformatics/btz872

DO - 10.1093/bioinformatics/btz872

M3 - SCORING: Journal article

C2 - 31782763

VL - 36

SP - 2189

EP - 2194

JO - BIOINFORMATICS

JF - BIOINFORMATICS

SN - 1367-4803

IS - 7

ER -