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GlobalANCOVA specifications

Information


Unique identifier OMICS_15700
Name GlobalANCOVA
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 3.48.0
Stability Stable
Requirements
AnnotationDbi, methods, KEGG.db, Biobase, corpcor, GO.db, vsn, annotate, Rgraphviz, GSEABase, golubEsets, hu6800.db, globaltest
Maintained Yes

Download


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Versioning


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Documentation


Maintainer


  • person_outline Manuela Hummel

Publication for GlobalANCOVA

GlobalANCOVA citations

 (4)
library_books

Investigating the concordance of Gene Ontology terms reveals the intra and inter platform reproducibility of enrichment analysis

2013
BMC Bioinformatics
PMCID: 3644270
PMID: 23627640
DOI: 10.1186/1471-2105-14-143

[…] identify significantly enriched gene sets []. In addition, other statistical methods including significance analysis of function and expression (SAFE) [], BayGO [], ProbCD [], EasyGO [], ProfCom [], GlobalANCOVA [], GOEAST [] and LRpath [] were also developed for enrichment analysis.Based on the methods mentioned above, researchers can subsequently reveal the pathological mechanism from the micro […]

library_books

Computational Biomarker Pipeline from Discovery to Clinical Implementation: Plasma Proteomic Biomarkers for Cardiac Transplantation

2013
PLoS Comput Biol
PMCID: 3617196
PMID: 23592955
DOI: 10.1371/journal.pcbi.1002963

[…] description of the statistical methods was described in previous subsections. All the statistical analysis was implemented using R version 2.10.1 with the following packages: limma (version 1.9.6) , GlobalAncova from Bioconductor (version 3.6.0) , , impute (version 1.24.0) , and ROCR (version 1.0-4) . […]

library_books

Multiple platform assessment of the EGF dependent transcriptome by microarray and deep tag sequencing analysis

2011
BMC Genomics
PMCID: 3141672
PMID: 21699700
DOI: 10.1186/1471-2164-12-326

[…] reliable and complete dataset of HeLa specific EGF-dependent regulated genes has been generated defining lists of genes not previously associated to EGF signaling. By applying the recently developed GlobalAncova test for pathway analysis of gene expression profiles, we used this dataset to gain insight into functional aspects and to explore higher order gene regulatory network relationships. […]

library_books

Heading Down the Wrong Pathway: on the Influence of Correlation within Gene Sets

2010
BMC Genomics
PMCID: 3091509
PMID: 20955544
DOI: 10.1186/1471-2164-11-574

[…] ulties in proper control of the false positive rate. It is worth noting that use of empirical covariance estimates is extremely challenging, especially when gene sets are larger than the sample size. GlobalANCOVA [] fits a linear model between each gene and the experimental covariates, and uses permutation testing to obtain empirical p-values. We found that GlobalANCOVA found no significant GO BP […]

Citations

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GlobalANCOVA institution(s)
IBE, University of Munich, University of Munich, Germany; Technische Fachhochschule Berlin, University of Munich, Germany; Department of Statistics, University of Munich, Germany
GlobalANCOVA funding source(s)
This work was supported by the NGFN project 01 GR 0459, BMBF, Germany.

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