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Protocols

CpGassoc specifications

Information


Unique identifier OMICS_00793
Name CpGassoc
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 2.60
Stability Stable
Requirements
qvalue, methods, R(≥2.10), nlme
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Richard T. Barfield <>

Publication for CpGassoc

CpGassoc citations

 (18)
library_books

Galactic Cosmic Radiation Induces Persistent Epigenome Alterations Relevant to Human Lung Cancer

2018
PMCID: 5928241
PMID: 29712937
DOI: 10.1038/s41598-018-24755-8

[…] all samples from a given exposure experiment were processed in parallel and on parallel chips with replicate samples randomized with respect to chip position., a linear mixed effects model, cpgassoc, was used to perform quality control and to identify dna methylation changes significantly associated with dose, or with time after exposure. the 56fe ion, 28si ion, and x ray exposed […]

library_books

A pilot investigation on DNA methylation modifications associated with complex posttraumatic symptoms in elderly traumatized in childhood

2017
PMCID: 5738217
PMID: 29258561
DOI: 10.1186/s13104-017-3082-y

[…] ones containing snps at the investigated cpg site or at a single base extension position. probes located on the sex chromosomes were also excluded. the minfi preprocessed data were analyzed with the cpgassoc package to assess correlation of dna methylation profiles with complex posttraumatic symptoms measured by the tsi scales []. age, gender, the estimated proportion of buccal epithelial cells, […]

library_books

Effects of maternal obesity on Wharton’s Jelly mesenchymal stromal cells

2017
PMCID: 5730612
PMID: 29242640
DOI: 10.1038/s41598-017-18034-1

[…] these were filtered out. in addition, probes having a detection p-value above 0.01 were filtered out, and 1921 probes were thus removed from analysis. the remaining 483591 probes were analysed. the cpgassoc r package and methlab software were used for differential methylation analysis together with the humanmethylation450 v1.2 manifest file containing cpg annotations. t-statistics […]

library_books

Epigenome wide association study of asthma and wheeze in childhood and adolescence

2017
PMCID: 5640901
PMID: 29046734
DOI: 10.1186/s13148-017-0414-7

[…] 13 mp2 [] to determine associations between cell types that were most likely to have a strong effect on results when adjusted for in ewas models., ewas were carried out in r version 3.0.2. using the cpgassoc package [] to model either asthma/wheeze status as the exposure and methylation (beta value) at either 7.5 or 16.5 years of age as the outcome. in addition to the cross-sectional ewas, […]

library_books

Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis

2017
PMCID: 5566454
PMID: 28827734
DOI: 10.1038/s41598-017-09335-6

[…] and qced using champ; the probe beta values were quantile-normalized using the ‘dasen’ method from the watermelon package. differential methylation on 425,694 probes post-qc was tested using the cpgassoc package, applying a linear model for tissue status at each probe, with individual id as covariate., following previous analyses, differentially methylated regions (dmrs) were defined […]

library_books

Effects of genistein supplementation on genome wide DNA methylation and gene expression in patients with localized prostate cancer

2017
PMCID: 5467777
PMID: 28560383
DOI: 10.3892/ijo.2017.4017

[…] discovery rates. the random seed used was 779948241. hierarchical clustering was performed using cluster software () and java treeview (). methylation microarray analysis was performed in r using cpgassoc module in bioconductor (). data from the 450k probes was filtered to those in which the maximum - minimum β-value was >0.2 to result in 160k probes for differential methylation analysis. […]


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CpGassoc institution(s)
Department of Bioinformatics and Biostatistics, School of Public Health, Emory University at Atlanta, GA, USA

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