globaltest statistics

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Citations per year

Number of citations per year for the bioinformatics software tool globaltest
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Tool usage distribution map

This map represents all the scientific publications referring to globaltest per scientific context
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Protocols

globaltest specifications

Information


Unique identifier OMICS_02084
Name globaltest
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 5.34.1
Stability Stable
Requirements
AnnotationDbi, methods, KEGG.db, graphics, Biobase, MASS, survival, GO.db, org.Hs.eg.db, vsn, annotate, Rgraphviz, GSEABase, golubEsets, boot, hu6800.db, lungExpression, penalized, gss, rpart
Maintained Yes

Versioning


No version available

Documentation


Publication for globaltest

globaltest citations

 (29)
library_books

Easy and efficient ensemble gene set testing with EGSEA

2017
F1000Res
PMCID: 5747338
PMID: 29333246
DOI: 10.5256/f1000research.13583.r27972

[…] eir median rank across the 11 methods. > baseMethods = egsea.base()[-2] > baseMethods [1] "camera" "safe" "gage" "padog" "plage" "zscore" [7] "gsva" "ssgsea" "globaltest" "ora" "fry" > > gsam = egsea.ma(expr=expr, group=group, + probe.annot = probe.annot, + design = design, + contrasts=contr.matrix, + gs.annots=gs.annots, + […]

call_split

Three dimensional tumor cell growth stimulates autophagic flux and recapitulates chemotherapy resistance

2017
PMCID: 5596581
PMID: 28837150
DOI: 10.1038/cddis.2017.398
call_split See protocol

[…] d by fitting a linear model using the limma package in R., In order to identify pathways that are differentially regulated between 2D and 3D (static and bioreactor system) cell cultures, we applied a globaltest. This test evaluates Gene Ontology (GO) terms (http://www.geneontology.org/) of the ‘Biological Process’ ontology.In addition, we sorted the regulated genes with the GO term ‘autophagy’ (GO […]

library_books

Radiographic endophenotyping in hip osteoarthritis improves the precision of genetic association analysis

2017
PMCID: 5530347
PMID: 27974301
DOI: 10.1136/annrheumdis-2016-210373

[…] gramming language after quality checks using Illumina Beadstudio analysis software (Illumina). Intensity values were normalised and absence of large-scale between-chip effects was confirmed using the Globaltest-package. Probes that were not optimally measured were removed (detection p>0.05 in more than 50% of the samples). All comparisons of the differential normalised probe expression levels betw […]

library_books

Combining multiple tools outperforms individual methods in gene set enrichment analyses

2016
Bioinformatics
PMCID: 5408797
PMID: 27694195
DOI: 10.1093/bioinformatics/btw623

[…] an rank was used as a scoring function and a bin width of 5 was used for the vote ranking. Eight GSE methods were used as base methods for the EGSEA analysis: camera, safe, gage, padog, zscore, gsva, globaltest and ora. The analysis was conducted on the MSigDB c2 collection (of 4722 gene sets) using the same machine that was mentioned earlier. The execution time varied between 182.1 s (single thre […]

library_books

Meta Analysis of Tumor Stem Like Breast Cancer Cells Using Gene Set and Network Analysis

2016
PLoS One
PMCID: 4752453
PMID: 26870956
DOI: 10.1371/journal.pone.0148818

[…] sets using Kernel-based Orthogonal Projections to Latent Structures (K-OPLS) []. From the four significant gene sets, we selected individual gene based on p-values and expression directions using the Globaltest R package [, , ]. Distinct from other meta-analysis, we selected individual markers which can explain the mechanisms underlying tumor stem-like breast cancer cells by applying gene set anal […]

library_books

Integrative enrichment analysis: a new computational method to detect dysregulated pathways in heterogeneous samples

2015
BMC Genomics
PMCID: 4641376
PMID: 26556243
DOI: 10.1186/s12864-015-2188-7

[…] mean of absolute values of weighted moderated gene t-scores where the gene weights are designed to be large for the genes appearing in few pathways and small for genes that appear in many pathways [].GLOBALTEST: it holds an assumption that, if a group of genes (e.g., pathway genes) can be used to predict the clinical outcome, the expression patterns of such gene group must differ for dissimilar cl […]


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globaltest institution(s)
Department of Medical Statistics, Leiden University Medical Center, Leiden, Netherlands; Mathematical Institute, Leiden University, Netherlands; Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, Netherlands

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