Publication

breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data

Porubsky, D., Sanders, A. D., Taudt, A., Colomé-Tatché, M., Lansdorp, P. M. & Guryev, V., 30-Aug-2019, In : Bioinformatics (Oxford, England).

Research output: Contribution to journalArticleAcademicpeer-review

APA

Porubsky, D., Sanders, A. D., Taudt, A., Colomé-Tatché, M., Lansdorp, P. M., & Guryev, V. (2019). breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data. Bioinformatics (Oxford, England). https://doi.org/10.1093/bioinformatics/btz681

Author

Porubsky, David ; Sanders, Ashley D ; Taudt, Aaron ; Colomé-Tatché, Maria ; Lansdorp, Peter M ; Guryev, Victor. / breakpointR : an R/Bioconductor package to localize strand state changes in Strand-seq data. In: Bioinformatics (Oxford, England). 2019.

Harvard

Porubsky, D, Sanders, AD, Taudt, A, Colomé-Tatché, M, Lansdorp, PM & Guryev, V 2019, 'breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data', Bioinformatics (Oxford, England). https://doi.org/10.1093/bioinformatics/btz681

Standard

breakpointR : an R/Bioconductor package to localize strand state changes in Strand-seq data. / Porubsky, David; Sanders, Ashley D; Taudt, Aaron; Colomé-Tatché, Maria; Lansdorp, Peter M; Guryev, Victor.

In: Bioinformatics (Oxford, England), 30.08.2019.

Research output: Contribution to journalArticleAcademicpeer-review

Vancouver

Porubsky D, Sanders AD, Taudt A, Colomé-Tatché M, Lansdorp PM, Guryev V. breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data. Bioinformatics (Oxford, England). 2019 Aug 30. https://doi.org/10.1093/bioinformatics/btz681


BibTeX

@article{322e6807ec304d1581c09b74c2f42b40,
title = "breakpointR: an R/Bioconductor package to localize strand state changes in Strand-seq data",
abstract = "MOTIVATION: Strand-seq is a specialized single-cell DNA sequencing technique centered around the directionality of single-stranded DNA. Computational tools for Strand-seq analyses must capture the strand-specific information embedded in these data.RESULTS: Here we introduce breakpointR, an R/Bioconductor package specifically tailored to process and interpret single-cell strand-specific sequencing data obtained from Strand-seq. We developed breakpointR to detect local changes in strand directionality of aligned Strand-seq data, to enable fine-mapping of sister chromatid exchanges, germline inversion and to support global haplotype assembly. Given the broad spectrum of Strand-seq applications we expect breakpointR to be an important addition to currently available tools and extend the accessibility of this novel sequencing technique.AVAILABILITY: R/Bioconductor package https://bioconductor.org/packages/breakpointR.",
author = "David Porubsky and Sanders, {Ashley D} and Aaron Taudt and Maria Colom{\'e}-Tatch{\'e} and Lansdorp, {Peter M} and Victor Guryev",
note = "{\circledC} The Author(s) (2019). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.",
year = "2019",
month = "8",
day = "30",
doi = "10.1093/bioinformatics/btz681",
language = "English",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",

}

RIS

TY - JOUR

T1 - breakpointR

T2 - an R/Bioconductor package to localize strand state changes in Strand-seq data

AU - Porubsky, David

AU - Sanders, Ashley D

AU - Taudt, Aaron

AU - Colomé-Tatché, Maria

AU - Lansdorp, Peter M

AU - Guryev, Victor

N1 - © The Author(s) (2019). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

PY - 2019/8/30

Y1 - 2019/8/30

N2 - MOTIVATION: Strand-seq is a specialized single-cell DNA sequencing technique centered around the directionality of single-stranded DNA. Computational tools for Strand-seq analyses must capture the strand-specific information embedded in these data.RESULTS: Here we introduce breakpointR, an R/Bioconductor package specifically tailored to process and interpret single-cell strand-specific sequencing data obtained from Strand-seq. We developed breakpointR to detect local changes in strand directionality of aligned Strand-seq data, to enable fine-mapping of sister chromatid exchanges, germline inversion and to support global haplotype assembly. Given the broad spectrum of Strand-seq applications we expect breakpointR to be an important addition to currently available tools and extend the accessibility of this novel sequencing technique.AVAILABILITY: R/Bioconductor package https://bioconductor.org/packages/breakpointR.

AB - MOTIVATION: Strand-seq is a specialized single-cell DNA sequencing technique centered around the directionality of single-stranded DNA. Computational tools for Strand-seq analyses must capture the strand-specific information embedded in these data.RESULTS: Here we introduce breakpointR, an R/Bioconductor package specifically tailored to process and interpret single-cell strand-specific sequencing data obtained from Strand-seq. We developed breakpointR to detect local changes in strand directionality of aligned Strand-seq data, to enable fine-mapping of sister chromatid exchanges, germline inversion and to support global haplotype assembly. Given the broad spectrum of Strand-seq applications we expect breakpointR to be an important addition to currently available tools and extend the accessibility of this novel sequencing technique.AVAILABILITY: R/Bioconductor package https://bioconductor.org/packages/breakpointR.

U2 - 10.1093/bioinformatics/btz681

DO - 10.1093/bioinformatics/btz681

M3 - Article

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

ER -

ID: 96511736