Genedata Expressionist statistics

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Genedata Expressionist specifications

Information


Unique identifier OMICS_00761
Name Genedata Expressionist
Software type Package/Module
Interface Command line interface
Restrictions to use License purchase required
Operating system Unix/Linux
License Commercial
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Genedata Expressionist Team <>

Genedata Expressionist in pipeline

2016
PMCID: 5158117
PMID: 27867160
DOI: 10.1264/jsme2.ME16107

[…] of 5,481 nucleotides, and the maximum contig had a length of 360,777 nucleotides. the total length of the 68 contigs was 372,707 nucleotides (). the mapping of reads was performed using the software genedata expressionist for genomic profiling version 9.1.4a and bwa-mem, according to the manufacturer’s protocol, and was visualized and confirmed using the software integrative genomic viewer […]


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Genedata Expressionist in publications

 (43)
PMCID: 5935921
PMID: 29728068
DOI: 10.1186/s12864-018-4691-0

[…] previous study [], were used. the sequenced reads were mapped onto the reference genome using the tophat software v2.0.14 [], and reads per kilobase per million (rpkm) values were computed using the genedata expressionist software v9.1.1a (genedata ag, basel, switzerland). genes with rpkm > 1 were regarded as expressed genes []., the genes involved in specific metabolic pathways […]

PMCID: 5740791
PMID: 29268762
DOI: 10.1186/s13073-017-0499-9

[…] of the first samples sequenced with a 100-bp paired-end mode showed that the library insert size was small. therefore, the remaining samples were sequenced with a 50-bp paired-end mode. using genedata expressionist® for genomic profiling v9.1, we established a bioinformatics pipeline for the detection of cancer specific differentially methylated regions (dmrs). the most promising dmrs […]

PMCID: 5740748
PMID: 29268796
DOI: 10.1186/s13073-017-0500-7

[…] digested dna was adapter ligated, bisulfite-modified, and polymerase chain reaction (pcr)-amplified. the libraries were sequenced on illumina’s hiseq 2500 with 50 bp or 100 bp paired-end mode. using genedata expressionist® for genomic profiling v9.1, we have established a bioinformatics pipeline for the detection of cancer-specific dmrs. the most promising dmrs have been taken forward […]

PMCID: 5788588
PMID: 29416720
DOI: 10.18632/oncotarget.22895

[…] sureselect xt reagent kit and sureselect human all exon kit v5 (agilent technologies, santa clara, ca). ngs was performed by use of hiseq 2500 (illumina inc., san diego, ca). data was analyzed by genedata expressionist (genedata ag, basel, switzerland). the integrative genomics viewer (igv, broad institute, cambridge, ma) was used for visualization of the genomic alignment data., […]

PMCID: 5799712
PMID: 28991225
DOI: 10.1038/onc.2017.325

[…] before rna extraction and profiling with affymetrix hugene-2.1st arrays. data are available in the geo database under gse92736. probe set intensities were condensed to meta-probe set levels in genedata expressionist 9.0 using robust multi-array (rma) algorithm followed by lowess normalization. a 2-group t-test was used to compare the treatment and control groups. the resulting p-values […]


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Genedata Expressionist review

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Catherine SIRVEN's avatar image No country

Catherine SIRVEN

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Desktop
Very convinient end user tool for data visualisation and Gene expression dicovery. A lot of parameters can be used. Stay user friendly. Probably not enough customisable for command line bioinformaticien but this is not the purpose of the tool.