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Number of citations per year for the bioinformatics software tool RNAither
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Protocols

RNAither specifications

Information


Unique identifier OMICS_12186
Name RNAither
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data RNAither provides a function to generate a suitable input text file for the pipeline from the experimental output data. It contains a header describing the experiment, and a table containing, for each well or spot, the spot number and type (e.g. control or empty), the siRNA and/or gene name, the signal intensities (default is two channels), the plate and experiment number and the position of the well on the plate, as well as, if available, SDs and/or background intensity of the signal values.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 2.28.0
Stability Stable
Requirements
limma, methods, R(>=2.10), biomaRt, geneplotter, RankProd, topGO, car, prada, splots
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Lars Kaderali

Publication for RNAither

RNAither citations

 (9)
library_books

ABHD5/CGI 58, the Chanarin Dorfman Syndrome Protein, Mobilises Lipid Stores for Hepatitis C Virus Production

2016
PLoS Pathog
PMCID: 4849665
PMID: 27124600
DOI: 10.1371/journal.ppat.1005568

[…] Statistical data analysis was performed in R (http://www.r-project.org). siRNA screening data was analysed using the Bioconductor package RNAither [], using lowess and negcontrol normalisation, and using p<0.05 as threshold for hit selection. Individual follow-up experiments (Figs and ) were statistically analysed using Welch’s t-test […]

library_books

Integrative Genomics Based Discovery of Novel Regulators of the Innate Antiviral Response

2015
PLoS Comput Biol
PMCID: 4618338
PMID: 26485378
DOI: 10.1371/journal.pcbi.1004553

[…] Plots, statistics and other calculations were done using custom Perl and SQL scripts, and the R statistical package [] with additional packages gplots [], ROCR [] and RNAither []. One-way ANOVA with Dunnett's post hoc test was performed using GraphPad Prism (GraphPad Software). […]

library_books

Impact of normalization methods on high throughput screening data with high hit rates and drug testing with dose–response data

2015
Bioinformatics
PMCID: 4653387
PMID: 26254433
DOI: 10.1093/bioinformatics/btv455

[…] . In addition to the B-score, a number of other noise reducing methods based on polynomial least squares fit have been published () and implemented in open source Bioconductor packages cellHTS () and RNAither () and platforms such as HitPick (). For example, the locally weighted scatterplot smoothing (Loess-fit) is based on fitting a distribution surface on the whole plate data matrix. Despite the […]

library_books

Human Genome Wide RNAi Screen Identifies an Essential Role for Inositol Pyrophosphates in Type I Interferon Response

2014
PLoS Pathog
PMCID: 3937324
PMID: 24586175
DOI: 10.1371/journal.ppat.1003981

[…] ty. siRNAs targeting IRF3 and MAVS were used as positive controls, and a non-targeting (NT) siRNA served as the negative control.The bioinformatics analysis of the siRNA screen was facilitated by the RNAither package of Bioconductor in R . The screen was performed in duplicate. The mean percent GFP-positive cells was calculated for each gene (the screen was performed in duplicate), and then a Z-sc […]

library_books

Robust RNAi enhancement via human Argonaute 2 overexpression from plasmids, viral vectors and cell lines

2013
Nucleic Acids Res
PMCID: 3834839
PMID: 24049077
DOI: 10.1093/nar/gkt836

[…] atio of plasma membrane-incorporated ts-O45-G to the total amount of expressed protein. A median of secretion rates in all cells was then deduced based on all acquired images in each well. R and the ‘RNAither' package (http://www.bioconductor.org/) were used for normalization of experimental replicates. For cross-experiment comparisons, the median of the negative control (‘All Stars’ siRNA) was su […]

library_books

Antiviral Stratagems Against HIV 1 Using RNA Interference (RNAi) Technology

2013
Evol Bioinform Online
PMCID: 3662398
PMID: 23761954
DOI: 10.4137/EBO.S11412

[…] esting correction methods., Examples include Applied Biosystems, Biotek, Cellomics, POwerMV, siRna, and some special libraries embedded in popular programming languages such as R software and Matlab. RNAither, a recently developed R library, generates lists of relevant genes and pathways from raw experimental data. However, given the increasing amount of information produced and their increasing c […]


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RNAither institution(s)
Viroquant Research Group Modeling, University of Heidelberg, Heidelberg, Germany; Theoretical Bioinformatics, German Cancer Research Center, Heidelberg, Germany
RNAither funding source(s)
German Federal Ministry of Education and Research, BMBF, grant number 01313923 (FORSYS/Viroquant)

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