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limmaGUI specifications

Information


Unique identifier OMICS_02027
Name limmaGUI
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.56.1
Stability Stable
Requirements
limma, methods, graphics, utils, grDevices, xtable, R2HTML, tcltk, tkrplot
Maintained Yes

Versioning


No version available

Documentation


Publication for limmaGUI

limmaGUI citations

 (31)
library_books

Adaptive Mistranslation Accelerates the Evolution of Fluconazole Resistance and Induces Major Genomic and Gene Expression Alterations in Candida albicans

2017
PMCID: 5549176
PMID: 28808688
DOI: 10.1128/mSphere.00167-17

[…] Arrays were scanned on an Agilent G2505C microarray scanner, and microarray scan data were extracted with Agilent feature extraction software.Raw gene expression microarray data were normalized with limmaGUI software (R/Bioconductor, Boston, MA) (). Differentially expressed genes (DEGs) were extracted with limma () by using a differential threshold of 1.5 and a false discovery rate-corrected P va […]

library_books

Key Components of Different Plant Defense Pathways Are Dispensable for Powdery Mildew Resistance of the Arabidopsis mlo2 mlo6 mlo12 Triple Mutant

2017
Front Plant Sci
PMCID: 5475338
PMID: 28674541
DOI: 10.3389/fpls.2017.01006

[…] e the probe values into probe set values, resulting in 22,811 normalized expression values per array. The R/Bioconductor (Gentleman et al., ) package limma (Smyth, ) with the graphical user interface limmaGUI (Wettenhall and Smyth, ) was employed to pre-process the raw microarray data. Analysis of variance (ANOVA) in combination with the false discovery rate (FDR) test method were applied to corre […]

call_split

Guanabenz Prevents d Galactosamine/Lipopolysaccharide Induced Liver Damage and Mortality

2017
Front Immunol
PMCID: 5468566
PMID: 28659918
DOI: 10.3389/fimmu.2017.00679
call_split See protocol

[…] s (Affymetrix GeneChip Mouse Gene 1.0 ST) and image scanning were performed according to the Affymetrix Expression Analysis Technical Manual. Gene Expression microarray raw data were normalized using limmaGUI software (R/Bioconductor, Boston, MA, USA). Data can be accessed through the GEO repository accession number GSE90831. Microarrays data were analyzed with the ingenuity pathway analysis (IPA) […]

library_books

Enhancing knowledge discovery from cancer genomics data with Galaxy

2017
GigaScience
PMCID: 5437943
PMID: 28327945
DOI: 10.1093/gigascience/gix015

[…] rning the utility of the associated with command-line interfaces but typically do not scale to large data sets. Examples of genomics tools offering web-accessible GUIs include BLAST [], VAGUE [], and limmaGUI []. However, beyond an inability to scale, web-based utilities pose several issues, including design inconsistency, redundant efforts in interface development, and the inability to automatica […]

library_books

limma powers differential expression analyses for RNA sequencing and microarray studies

2015
Nucleic Acids Res
PMCID: 4402510
PMID: 25605792
DOI: 10.1093/nar/gkv007

[…] he limma package is used as a building block or as the underlying computational engine by a number of software projects designed to provide user-interfaces for gene expression data analysis including limmaGUI (), affylmGUI (), WebArray (), RACE (), CarmaWEB (), Goulphar (), MAGMA (), Asterias (), GenePattern (), GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r), the EBI expression atlas (), Guide () a […]

library_books

Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b overexpression enhances water productivity, resistance to drought, and infection

2013
J Exp Bot
PMCID: 3733161
PMID: 23828547
DOI: 10.1093/jxb/ert185

[…] rom rosettes of four pooled plants, and the comparison of Col-0 versus HSFA2Ox was carried out using the CATMA (version 3) microarray (). Normalization and analysis of the array was carried out using LimmaGUI, a graphical front end for the limma (Linear Models for MicroArray; ) package for R available from Bioconductor (http://www.bioconductor.org). […]

Citations

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limmaGUI institution(s)
Division of Genetics and Bioinformatics, Walter and Eliza Hall Institute of Medical Research, Parkville, Australia

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