How to cite the Bioconductor package ideal
ideal is a popular Bioconductor package that is available at https://bioconductor.org/packages/ideal. By citing R packages in your paper you lay the grounds for others to be able to reproduce your analysis and secondly you are acknowledging the time and work people have spent creating the package.
APA citation
Formatted according to the APA Publication Manual 7th edition. Simply copy it to the References page as is.
The minimal requirement is to cite the R package in text along with the version number. Additionally, you can include the reference list entry the authors of the ideal package have suggested.
Example of an in-text citation
Analysis of the data was done using the ideal package (v1.14.0; Marini et al., 2020).
Reference list entry
Marini, F., Linke, J., & Binder, H. (2020). ideal: an R/Bioconductor package for Interactive Differential Expression Analysis. bioRxiv. https://doi.org/10.1101/2020.01.10.901652
Vancouver citation
Formatted according to Vancouver style. Simply copy it to the references section as is.
Example of an in-text citation
Analysis of the data was done using the ideal package v1.14.0 (1).
Reference list entry
1.Marini F, Linke J, Binder H. ideal: an R/Bioconductor package for Interactive Differential Expression Analysis [Internet]. bioRxiv; 2020. Available from: http://dx.doi.org/10.1101/2020.01.10.901652
BibTeX
Reference entry in BibTeX format. Simply copy it to your favorite citation manager.
@UNPUBLISHED{Marini2020-hb,
title = "ideal: an {R/Bioconductor} package for Interactive
Differential Expression Analysis",
author = "Marini, Federico and Linke, Jan and Binder, Harald",
abstract = "AbstractBackgroundRNA sequencing (RNA-seq) is an ever
increasingly popular tool for transcriptome profiling. A key
point to make the best use of the available data is to provide
software tools that are easy to use but still provide
flexibility and transparency in the adopted methods. Despite
the availability of many packages focused on detecting
differential expression, a method to streamline this type of
bioinformatics analysis in a comprehensive, accessible, and
reproducible way is lacking.ResultsWe developed the ideal
software package, which serves as a web application for
interactive and reproducible RNA-seq analysis, while producing
a wealth of visualizations to facilitate data interpretation.
ideal is implemented in R using the Shiny framework, and is
fully integrated with the existing core structures of the
Bioconductor project. Users can perform the essential steps of
the differential expression analysis work-flow in an assisted
way, and generate a broad spectrum of publication-ready
outputs, including diagnostic and summary visualizations in
each module, all the way down to functional analysis. ideal
also offers the possibility to seamlessly generate a full HTML
report for storing and sharing results together with code for
reproducibility.Conclusionideal is distributed as an R package
in the Bioconductor project
(http://bioconductor.org/packages/ideal/), and provides a
solution for performing interactive and reproducible analyses
of summarized RNA-seq expression data, empowering researchers
with many different profiles (life scientists, clinicians, but
also experienced bioinformaticians) to make the ideal use of
the data at hand.",
institution = "bioRxiv",
month = jan,
year = 2020,
url = "http://dx.doi.org/10.1101/2020.01.10.901652",
doi = "10.1101/2020.01.10.901652"
}
RIS
Reference entry in RIS format. Simply copy it to your favorite citation manager.
TY - INPR
AU - Marini, Federico
AU - Linke, Jan
AU - Binder, Harald
TI - ideal: an R/Bioconductor package for Interactive Differential Expression
Analysis
PY - 2020
DA - 2020/1/11
AB - AbstractBackgroundRNA sequencing (RNA-seq) is an ever increasingly popular
tool for transcriptome profiling. A key point to make the best use of the
available data is to provide software tools that are easy to use but still
provide flexibility and transparency in the adopted methods. Despite the
availability of many packages focused on detecting differential
expression, a method to streamline this type of bioinformatics analysis in
a comprehensive, accessible, and reproducible way is lacking.ResultsWe
developed the ideal software package, which serves as a web application
for interactive and reproducible RNA-seq analysis, while producing a
wealth of visualizations to facilitate data interpretation. ideal is
implemented in R using the Shiny framework, and is fully integrated with
the existing core structures of the Bioconductor project. Users can
perform the essential steps of the differential expression analysis
work-flow in an assisted way, and generate a broad spectrum of
publication-ready outputs, including diagnostic and summary visualizations
in each module, all the way down to functional analysis. ideal also offers
the possibility to seamlessly generate a full HTML report for storing and
sharing results together with code for reproducibility.Conclusionideal is
distributed as an R package in the Bioconductor project
(http://bioconductor.org/packages/ideal/), and provides a solution for
performing interactive and reproducible analyses of summarized RNA-seq
expression data, empowering researchers with many different profiles (life
scientists, clinicians, but also experienced bioinformaticians) to make
the ideal use of the data at hand.
DO - 10.1101/2020.01.10.901652
UR - http://dx.doi.org/10.1101/2020.01.10.901652
ER -
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