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 in publications

 (22)
PMCID: 5248646
PMID: 27668839
DOI: 10.1002/yea.3211

[…] 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 […]

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 […]

PMCID: 4402510
PMID: 25605792
DOI: 10.1093/nar/gkv007

[…] 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)., […]

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

[…] 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 […]

PMCID: 4218774
PMID: 25365506
DOI: 10.1371/journal.pone.0111589

[…] 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 […]


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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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