Protocol for generating customizable and reproducible plots of sequencing coverage data using the seqNdisplayR package

Søren Lykke-Andersen; Jérôme O. Rouvière; Manfred Schmid; Maria Gockert; Torben Heick Jensen

doi:10.1016/j.xpro.2024.102960

Protocol for generating customizable and reproducible plots of sequencing coverage data using the seqNdisplayR package

Søren Lykke-Andersen^*, Jérôme O. Rouvière, Manfred Schmid, Maria Gockert, Torben Heick Jensen^*

^*Corresponding author af dette arbejde

Institut for Molekylærbiologi og Genetik - RNA-biologi og -innovation

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

2 Citationer (Scopus)

Abstract

The widespread usage of next-generation sequencing methods for functional genomics studies requires standardized tools for consistent visualization of the associated data. Here, we present seqNdisplayR, an R package for plotting standard sequencing data coverage within a genomic region of interest in a customizable and reproducible manner. We describe steps for installing software, preparing data files, choosing options, and plotting data. This tool is readily available for users with no prior experience with R through the “Shiny app” interface. For complete details on the use and execution of this protocol, please refer to Lykke-Andersen et al.,¹ Gockert et al.,² and Rouviere et al.³

Originalsprog	Engelsk
Artikelnummer	102960
Tidsskrift	STAR Protocols
Vol/bind	5
Nummer	2
DOI	https://doi.org/10.1016/j.xpro.2024.102960
Status	Udgivet - jun. 2024

Adgang til dokumentet

10.1016/j.xpro.2024.102960Licens: CC BY-NC

Citationsformater

@article{f477509de10d4cbc801c82f6b2c5c6a8,

title = "Protocol for generating customizable and reproducible plots of sequencing coverage data using the seqNdisplayR package",

abstract = "The widespread usage of next-generation sequencing methods for functional genomics studies requires standardized tools for consistent visualization of the associated data. Here, we present seqNdisplayR, an R package for plotting standard sequencing data coverage within a genomic region of interest in a customizable and reproducible manner. We describe steps for installing software, preparing data files, choosing options, and plotting data. This tool is readily available for users with no prior experience with R through the “Shiny app” interface. For complete details on the use and execution of this protocol, please refer to Lykke-Andersen et al.,1 Gockert et al.,2 and Rouviere et al.3",

keywords = "ChIP, ChIP-seq, Chromatin immunoprecipitation, Gene Expression, RNA-seq, Sequencing",

author = "S{\o}ren Lykke-Andersen and Rouvi{\`e}re, {J{\'e}r{\^o}me O.} and Manfred Schmid and Maria Gockert and Jensen, {Torben Heick}",

note = "Publisher Copyright: {\textcopyright} 2024 The Author(s)",

year = "2024",

month = jun,

doi = "10.1016/j.xpro.2024.102960",

language = "English",

volume = "5",

journal = "STAR Protocols",

issn = "2666-1667",

publisher = "Cell Press",

number = "2",

}

Protocol for generating customizable and reproducible plots of sequencing coverage data using the seqNdisplayR package. / Lykke-Andersen, Søren ; Rouvière, Jérôme O.; Schmid, Manfred et al.
I: STAR Protocols, Bind 5, Nr. 2, 102960, 06.2024.

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avis › Tidsskriftartikel › Forskning › peer review

TY - JOUR

T1 - Protocol for generating customizable and reproducible plots of sequencing coverage data using the seqNdisplayR package

AU - Lykke-Andersen, Søren

AU - Rouvière, Jérôme O.

AU - Schmid, Manfred

AU - Gockert, Maria

AU - Jensen, Torben Heick

PY - 2024/6

Y1 - 2024/6

N2 - The widespread usage of next-generation sequencing methods for functional genomics studies requires standardized tools for consistent visualization of the associated data. Here, we present seqNdisplayR, an R package for plotting standard sequencing data coverage within a genomic region of interest in a customizable and reproducible manner. We describe steps for installing software, preparing data files, choosing options, and plotting data. This tool is readily available for users with no prior experience with R through the “Shiny app” interface. For complete details on the use and execution of this protocol, please refer to Lykke-Andersen et al.,1 Gockert et al.,2 and Rouviere et al.3

AB - The widespread usage of next-generation sequencing methods for functional genomics studies requires standardized tools for consistent visualization of the associated data. Here, we present seqNdisplayR, an R package for plotting standard sequencing data coverage within a genomic region of interest in a customizable and reproducible manner. We describe steps for installing software, preparing data files, choosing options, and plotting data. This tool is readily available for users with no prior experience with R through the “Shiny app” interface. For complete details on the use and execution of this protocol, please refer to Lykke-Andersen et al.,1 Gockert et al.,2 and Rouviere et al.3

KW - ChIP

KW - ChIP-seq

KW - Chromatin immunoprecipitation

KW - Gene Expression

KW - RNA-seq

KW - Sequencing

U2 - 10.1016/j.xpro.2024.102960

DO - 10.1016/j.xpro.2024.102960

M3 - Journal article

C2 - 38502686

AN - SCOPUS:85188834623

SN - 2666-1667

VL - 5

JO - STAR Protocols

JF - STAR Protocols

IS - 2

M1 - 102960

ER -

Protocol for generating customizable and reproducible plots of sequencing coverage data using the seqNdisplayR package

Abstract

Adgang til dokumentet

Fingeraftryk

Citationsformater