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Goulphar specifications

Information


Unique identifier OMICS_14404
Name Goulphar
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output format PDF
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1.3
Stability No
Requirements
marray, limma, convert, hexbin
Maintained No

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Publication for Goulphar

Goulphar citations

 (25)
library_books

Drawing Links from Transcriptome to Metabolites: The Evolution of Aroma in the Ripening Berry of Moscato Bianco (Vitis vinifera L.)

2017
Front Plant Sci
PMCID: 5432621
PMID: 28559906
DOI: 10.3389/fpls.2017.00780

[…] ity distributions), median intensity gene expression data without background subtraction were normalized by a global lowess method followed by a print-tip median method with a modified version of the Goulphar script version 1.1.2 (Lemoine et al., ). Differentially expressed probes (DEPs) with a false discovery rate (FDR) < 1% and a cut-off of 2-fold change (FC) were identified with the R/Bioconduc […]

library_books

Proteomic and genomic characterization of a yeast model for Ogden syndrome

2016
PMCID: 5248646
PMID: 27668839
DOI: 10.1002/yea.3211

[…] were hybridized to 8 × 15 k yeast microarrays and scanned using a 2 µm Agilent microarray scanner. The images were analysed using the feature extraction software and normalized by global lowess using Goulphar. For each gene, the Cy5/Cy3 ratios corresponding to the duplicated probes were averaged. The averaged log2 ratios and the standard deviation between the two replicates were calculated for eac […]

library_books

Ssn6 Defines a New Level of Regulation of White Opaque Switching in Candida albicans and Is Required For the Stochasticity of the Switch

2016
MBio
PMCID: 4742700
PMID: 26814177
DOI: 10.1128/mBio.01565-15

[…] 020166), and arrays were scanned using a GenePix 4000B microarray scanner. Array images were gridded using GenePix Pro version 7, and global LOWESS normalization was performed for each array using a Goulphar script written for R (). Normalized data for independent probes corresponding to the same ORF was then collapsed using a Python script. Processed, transformed data for key comparisons can be […]

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

[…] ing 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 () and Degust (http://www.vicbioinformatics.com/degust). […]

library_books

Kinetic transcriptome analysis reveals an essentially intact induction system in a cellulase hyper producer Trichoderma reesei strain

2014
Biotechnol Biofuels
PMCID: 4279801
PMID: 25550711
DOI: 10.1186/s13068-014-0173-z

[…] nufactured by Agilent and designed using the Teolenn software have been described previously [,].The data were normalized without background subtraction by the global lowess method performed with the Goulphar software []. The background threshold was calculated by adding two standard deviations to the average intensity of all the “not found” features. For each probe, the log2 hybridization ratio w […]

call_split

Role of the DHH1 Gene in the Regulation of Monocarboxylic Acids Transporters Expression in Saccharomyces cerevisiae

2014
PLoS One
PMCID: 4218774
PMID: 25365506
DOI: 10.1371/journal.pone.0111589
call_split See protocol

[…] 337). The microarray experiments were conducted as previously described . Raw data were normalized using global lowess followed by print-tip median methods, with background removal, as implemented in Goulphar . Experiments were carried out 2 times, with dye swapping. The microarray data are available in and fully available at the GEO database (accession number: GSE60983). The statistical signific […]

Citations

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Goulphar institution(s)
IFR36, Plate-forme Transcriptome, École Normale Supérieure, Paris, France; INSERM U784, École Normale Supérieure, Paris, France
Goulphar funding source(s)
This work was partly supported by the French RNG (Genopole National Network).

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