DCGL protocols

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DCGL specifications

Information


Unique identifier OMICS_12492
Name DCGL
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Version 2.1.2
Stability No
Source code URL https://cran.r-project.org/web/packages/DCGL/index.html
Maintained No

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Publications for DCGL

DCGL in pipelines

 (2)
2017
PMCID: 5588007
PMID: 28927082
DOI: 10.3892/ol.2017.6625

[…] associated biological processes, cellular components and molecular functions in a species-independent manner. the kegg database is used to display the biochemical pathways of the degs of interest., dcgl is a package that may serve as an effective tool for differential coexpression analysis (dcea). dcea determines the change of expression correlation of gene pairs and aids the investigation […]

2017
PMCID: 5588007
PMID: 28927082
DOI: 10.3892/ol.2017.6625

[…] of genes and genomes (kegg) pathway analyses were performed via the database for annotation, visualization and integrated discovery. differentially coexpressed pairs were identified by the dcgl package of r. the subsequent protein-protein interaction (ppi) networks and gene coexpression networks were constructed by the search tool for the retrieval of interacting genes/proteins […]


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DCGL in publications

 (15)
PMCID: 5776326
PMID: 29387060
DOI: 10.3389/fimmu.2017.01992

[…] using limma r package (). all the probes from each of the microarray platforms were filtered out for significant low expression/variation (p < 0.05) using the “variancebasedfilter” function from dcgl r package (). the remaining probes were mapped to ensembl gene identifiers and probes’ expression was collapsed to gene-level expression using “collapserows” function with default parameters […]

PMCID: 5783521
PMID: 29257233
DOI: 10.3892/mmr.2017.8213

[…] and involved pathways of the degs, kyoto encyclopedia of genes and genomes (kegg) pathway enrichment analysis was performed based on the webgestal database with the threshold of p<0.05 ()., dcgl was an r package for identifying differentially co-expressed genes and links from gene expression microarray data (). it could examine the expression correlation based on the exact co-expression […]

PMCID: 5588007
PMID: 28927082
DOI: 10.3892/ol.2017.6625

[…] associated biological processes, cellular components and molecular functions in a species-independent manner. the kegg database is used to display the biochemical pathways of the degs of interest., dcgl is a package that may serve as an effective tool for differential coexpression analysis (dcea). dcea determines the change of expression correlation of gene pairs and aids the investigation […]

PMCID: 5424481
PMID: 28529955
DOI: 10.1155/2017/8347085

[…] specific p values. modules with p value < 0.01 were considered as significantly differentially coexpressed., the differential coexpression analysis (dcea) was implemented by using r package dcgl, which is a useful tool to identify differentially coexpressed genes (dcgs) and differentially coexpressed links (dcls) [–]. the r function dce was applied and then the p values were adjusted […]

PMCID: 5009532
PMID: 27586240
DOI: 10.1186/s12918-016-0315-y

[…] oligodendroglioma grade ii, oiii oligodendroglioma grade iii, oa oligoastrocytoma, oaii oligoastrocytoma grade ii, oaiii oligoastrocytoma grade iii, pa pilocytic astrocytoma, we developed r package dcgl v2.0 for dcea and dra in our previous work [, ], which were used in the present study to detect differentially coexpressed genes and differentially regulated genes in glioma. we used r package […]


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DCGL institution(s)
Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA; Departments of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN, USA; Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA; Bioinformatics Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China; School of Biotechnology, East China University of Science and Technology, Shanghai, China; Shanghai Center for Bioinformation Technology, Shanghai Industrial Technology Institute, Shanghai, China

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