DiffCorr protocols

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DiffCorr specifications

Information


Unique identifier OMICS_12493
Name DiffCorr
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 0.4.1
Stability Stable
Requirements
pcaMethods, igraph, fdrtool, multtest
Maintained Yes

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Documentation


Maintainer


  • person_outline Atsushi Fukushima <>

Publication for DiffCorr

DiffCorr in pipeline

2016
PMCID: 5585989
PMID: 28062755
DOI: 10.1093/gbe/evw280

[…] species. the distribution of p-values was controlled for a false discovery rate (q-value) by the bh method () at α = 0.05., differentially coexpressed gene pairs were detected using the r package diffcorr (). briefly, the pearson correlation coefficient was calculated for each pair of genes, and fisher’s z-test was used to identify significant differential correlations between any two […]


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DiffCorr in publications

 (6)
PMCID: 5920388
PMID: 29725417
DOI: 10.3892/ol.2018.8221

[…] were used to search for highly co-expressed genes (absolute correlation coefficient |r|>0.85, p<0.01) in the deg set in which seed genes were ruled out in each stage. the software package diffcorr (https://sourceforge.net/projects/diffcorr/, version 0.4.1, slashdot media and dice, inc., san jose, ca, usa) () in r language was used to search for the differential correlation gene pairs […]

PMCID: 5681815
PMID: 29151892
DOI: 10.1186/s13040-017-0152-6

[…] it is uncertain which metric could be the best to detect differential co-expression networks because they have been applied only to specific datasets. in addition, some published packages such as diffcorr [] and diffcoex [] do not allow the evaluation of other metrics., therefore, in this paper, we aim to objectively compare the performance of different metrics under a well-controlled […]

PMCID: 5244536
PMID: 28103954
DOI: 10.1186/s13104-016-2331-9

[…] for the purpose of testing dc including pearson’s, spearman’s, biweight midcorrelation (bwmc) and a sparse compositional correlation method sparcc []., there are two r packages available for dc, diffcorr and ebcoexpress [, ]. these packages also provide functions to create graphs or networks of the data in addition to gene module analysis. to complement these existing packages, our work also […]

PMCID: 5056366
PMID: 27721457
DOI: 10.1038/srep35064

[…] with changed correlational relationships. based on fisher’s z-test, fukushima et al. explored tomato gene function via differential coexpression analysis. later, they published an r package called diffcorr to identify differential coexpression gene pairs. yang et al. implemented several methods in the r package dcgl to identify differential coexpression gene pairs, differentially coexpressed […]

PMCID: 4562606
PMID: 26396492
DOI: 10.4137/BMI.S29511

[…] of highly connected genes to additional information such as single-nucleotide polymorphisms (snps) as well as proteomic and clinical data. other correlation-based approaches, such as the r package diffcorr, can be used to focus on differences in patterns of relationships between two physiological conditions. other tools such as metamapr incorporate correlation analysis with other relationships […]


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DiffCorr institution(s)
RIKEN Plant Science Center, Kanagawa, Japan

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