DEDS statistics

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Citations per year

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

This map represents all the scientific publications referring to DEDS per scientific context
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Associated diseases

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DEDS specifications

Information


Unique identifier OMICS_02002
Name DEDS
Alternative name Differential Expression via Distance Summary
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.54.0
Stability Stable
Requirements
R(>=1.7.0)
Maintained Yes

Versioning


No version available

Documentation


DEDS citations

 (5)
library_books

The Ability of Different Imputation Methods to Preserve the Significant Genes and Pathways in Cancer

2017
PMCID: 5828654
PMID: 29247873
DOI: 10.1016/j.gpb.2017.08.003

[…] ated for their ability to detect the crucial genes involved in cancers. Five well-known methods were applied to acquire the significant genes from the original and imputed datasets. These include the differential expression via distance summary (DEDS) , empirical Bayes analyses of microarrays (EBAM) , Limma , multiple testing (MULTTEST) , , and significance analysis of microarrays (SAM) , which ar […]

library_books

Gene expression analysis supports tumor threshold over 2.0 cm for T category breast cancer

2016
EURASIP J Bioinform Syst Biol
PMCID: 4746218
PMID: 26900390
DOI: 10.1186/s13637-015-0034-5

[…] conditions, methods include vote counting, combining ranks, p values, and effect sizes []. Campain and Yang provided an intuitive measure, called meta differential expression via distance synthesis (mDEDS) [], using DE via distance synthesis (DEDS) [] to aggregate multiple DE measurements. The performance of mDEDS was compared with existing meta-analysis methods, such as Fisher’s inverse chi-squar […]

library_books

Pathway Centric Integrative Analysis Identifies RRM2 as a Prognostic Marker in Breast Cancer Associated with Poor Survival and Tamoxifen Resistance123

2014
PMCID: 4198742
PMID: 25016594
DOI: 10.1016/j.neo.2014.05.007

[…] y comparing luminal and basal subtypes coupled with False discovery rate (FDR) adjustment (adjusted P values < .2) using the Benjamini Hochberg (BH) method along with estimated fold change using the Differential Expression via Distance Summary (DEDS) package . […]

library_books

Algebraic Comparison of Partial Lists in Bioinformatics

2012
PLoS One
PMCID: 3355159
PMID: 22615778
DOI: 10.1371/journal.pone.0036540

[…] d t statistics. The FC of a given gene is defined here as the ratio of the average expression value computed over the two groups of samples. All filtering statistics are computed by using the package DEDS in the BioConductor extension of the statistical environment R .Reliability of a method over another is a debated issue in literature: while some authors believe that the lists coming from usin […]

library_books

Comparison study of microarray meta analysis methods

2010
BMC Bioinformatics
PMCID: 2922198
PMID: 20678237
DOI: 10.1186/1471-2105-11-408

[…] To establish the success of mDEDS as a meta-analysis method beyond the capabilities of DEDS, DEDS and mDEDS are compared. The strength of DEDS comes from its ability to synthesise results from a range of statistics, mDEDS goes be […]


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