omicade4 protocols

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omicade4 specifications

Information


Unique identifier OMICS_17512
Name omicade4
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 1.21.0
Stability Stable
Requirements
BiocStyle, R(>=3.0.0), ade4, made4
Maintained Yes

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Documentation


Maintainer


  • person_outline Chen Meng <>

omicade4 in pipeline

2016
PMCID: 5341331
PMID: 27894104
DOI: 10.18632/oncotarget.13569

[…] all three datasets were excluded from this analysis, leaving 56 samples in total. differences between samples and molecular assays were analyzed and visualized with co-inertia analysis using the r omicade4 package [] in the r statistical framework., to identify proteins previously found in evs, the vesiclepedia database of vesicular proteins was downloaded (version 3, 9 jan 2015) […]


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omicade4 in publications

 (6)
PMCID: 5900040
PMID: 29686662
DOI: 10.3389/fmicb.2018.00699

[…] multiple co-inertia analysis (mcia) () was performed to identify the changing trends of microbial communities in different tillage treatments and soil layers. mcia was implemented using the omicade4 package () in r (version 3.4.0). heatmaps and venn diagrams were drawn using the gplots library in r to show the distribution of microbial communities in different soil depths and tillage […]

PMCID: 5789592
PMID: 29378511
DOI: 10.1186/s12870-018-1239-z

[…] metabolite levels to functional metabolic pathways in the drought-treated groups, compared to those in the control groups., the mcoa was performed using the bioconductor software package omicade4 []. for consistency, we selected 1-, 2-, and 24-h treatments as the drought treatment groups, and 0 h as the control group. the 0-h and 24-h metabolomic profiles were used as the control […]

PMCID: 5171704
PMID: 27991589
DOI: 10.1038/srep37855

[…] in order to explore the relationship between gm and non-gm varieties. second, we performed a multiple co-inertia analysis (mcia), using the language and statistical environment r together with the omicade4 package, in order to integrate multiple omics datasets where the same tissue have been assayed multiple times (in this case, proteomics and metabolomics)., pairwise welch’s t-tests […]

PMCID: 5341331
PMID: 27894104
DOI: 10.18632/oncotarget.13569

[…] all three datasets were excluded from this analysis, leaving 56 samples in total. differences between samples and molecular assays were analyzed and visualized with co-inertia analysis using the r omicade4 package [] in the r statistical framework., to identify proteins previously found in evs, the vesiclepedia database of vesicular proteins was downloaded (version 3, 9 jan 2015) […]

PMCID: 4945831
PMID: 26969681
DOI: 10.1093/bib/bbv108

[…] matrices and re-iterated until the desired number of dimensions is reached. therefore, the computation time strongly depends on the number of desired dimensions. mcia is implemented in the r package omicade4 and has been applied to the integrative analysis of transcriptomic and proteomic data sets from the nci-60 cell lines []., gcca [] is a generalization of cca to k-table analysis []. […]


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