rsgcc statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Gene expression clustering chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

rsgcc specifications

Information


Unique identifier OMICS_07364
Name rsgcc
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data A clustered gene expression pattern.
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0, GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.6
Stability Stable
Requirements
gplots, grDevices, fBasics, bigmemory, snowfall, stringr, gWidgetsRGtk2, R(≥2.15.1), gWidgets, biwt, cairoDevice, minerva, parmigene, ctc
Source code URL https://cran.r-project.org/src/contrib/rsgcc_1.0.6.tar.gz
Maintained Yes

Download


Versioning


Add your version

Documentation


Maintainer


  • person_outline Chuang Ma <>

Publication for rsgcc

rsgcc in pipelines

 (2)
2018
PMCID: 5902692
PMID: 29692794
DOI: 10.3389/fpls.2018.00470

[…] regulated by sulfate in at least two different experiments. we then calculated the pearson correlation coefficients between each gene pair across all selected experiments using the r package rsgcc (). for network construction, an absolute correlation threshold of 0.81 was selected based on the best fit of the scale-free topology, as described previously (). the gene co-expression network […]

2017
PMCID: 5502274
PMID: 28740499
DOI: 10.3389/fpls.2017.01124

[…] patterns, respectively. empirical p-value of pearson correlation coefficient (pcc) values (statistical significance) of dataset1 and dataset2 were estimated by 1,000 permutations using the ‘rsgcc’ package (). enrichment for cre in the gene promoters (1 kb upstream of the 5′ utr or tss) of each wgcna co-response modules was conducted as described previously (; ). known cres of 6-, 7-, […]


To access a full list of citations, you will need to upgrade to our premium service.

rsgcc in publications

 (7)
PMCID: 5902692
PMID: 29692794
DOI: 10.3389/fpls.2018.00470

[…] regulated by sulfate in at least two different experiments. we then calculated the pearson correlation coefficients between each gene pair across all selected experiments using the r package rsgcc (). for network construction, an absolute correlation threshold of 0.81 was selected based on the best fit of the scale-free topology, as described previously (). the gene co-expression network […]

PMCID: 5816651
PMID: 29453355
DOI: 10.1038/s41598-018-21377-y

[…] both containing 25 contrasts each, using deseq2 with previously established pipelines., three gene co-expression networks were constructed using the gcc as the co-expression similarity index in the rsgcc package. one condition-independent network (datasetci) and two condition-dependent/specific networks (using dataseta and datasetb) were queried separately for the top 100 co-expressed gene […]

PMCID: 5558714
PMID: 28810830
DOI: 10.1186/s12862-017-1036-6

[…] in the identification of 3380 tissue-specific lincrnas (fig. , additional file : figure s3d and additional file ). secondly, 534 further tissue-specific lincrnas were obtained by utilizing the ‘rsgcc’ package in r software [] (methods), and were all included in the tsi set (fig. and additional file )., tissue-specific lincrnas can augment tissue-specific gene signatures []. thus, […]

PMCID: 5502274
PMID: 28740499
DOI: 10.3389/fpls.2017.01124

[…] patterns, respectively. empirical p-value of pearson correlation coefficient (pcc) values (statistical significance) of dataset1 and dataset2 were estimated by 1,000 permutations using the ‘rsgcc’ package (). enrichment for cre in the gene promoters (1 kb upstream of the 5′ utr or tss) of each wgcna co-response modules was conducted as described previously (; ). known cres of 6-, 7-, […]

PMCID: 4802899
PMID: 27001212
DOI: 10.1186/s12870-016-0760-1

[…] networks were constructed for three monoterpenes (linalool, nerol, and α-terpineol) considering the top 100 correlating genes. all calculations and permutation tests were performed in r using the ‘rsgcc’ package []., promoter motif enrichment analysis was conducted as described previously in ma et al. []. a total of 29,839 grapevine promoter sequences (1 kb upstream of the 5′ utr) based […]


To access a full list of publications, you will need to upgrade to our premium service.

rsgcc institution(s)
School of Plant Sciences, University of Arizona, Tucson, AZ, USA

rsgcc reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review rsgcc