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 for this work

Department of Molecular Biology and Genetics - RNA Biology and Innovation

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › peer-review

3 Citations (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

Original language	English
Article number	102960
Journal	STAR Protocols
Volume	5
Issue	2
DOIs	https://doi.org/10.1016/j.xpro.2024.102960
Publication status	Published - Jun 2024

Keywords

ChIP
ChIP-seq
Chromatin immunoprecipitation
Gene Expression
RNA-seq
Sequencing

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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",

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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.
In: STAR Protocols, Vol. 5, No. 2, 102960, 06.2024.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaper › Journal article › Research › 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

Keywords

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