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Goulphar specifications


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
marray, limma, convert, hexbin
Maintained No




No version available



This tool is not available anymore.

Publication for Goulphar

Goulphar citations


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

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 […]


Proteomic and genomic characterization of a yeast model for Ogden syndrome

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 […]


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

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 […]


limma powers differential expression analyses for RNA sequencing and microarray studies

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). […]


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

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 […]


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

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 […]


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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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