wateRmelon statistics
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wateRmelon specifications
Information
| Unique identifier | OMICS_02039 |
|---|---|
| Name | wateRmelon |
| 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 | 1.24.0 |
| Stability | Stable |
| Requirements |
Biobase
|
| Maintained | Yes |
Versioning
No version available
Documentation
Publication for wateRmelon
wateRmelon citations
(46)Impact on birth weight of maternal smoking throughout pregnancy mediated by DNA methylation
[…] Quality control (QC) and all statistical analyses were performed using the R version 3.2.5 statistical analysis software [], and the R-packages minfi [], wateRmelon [], Enmix [], sva [], limma [], and mediation []. […]
Epigenome Wide Association Study of Soluble Tumor Necrosis Factor Receptor 2 Levels in the Framingham Heart Study
[…] included 2270 samples from the remainder of the offspring cohort participants. DNA methylation results underwent normalization within laboratory batches using the DASEN methodology implemented in the wateRmelon package () in R (version 3.0.2). We excluded samples with missing rate > 1%, poor single nucleotide polymorphism (SNP) matching to the 65 SNP control probe locations, and outliers by multi- […]
A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip
[…] processing, there were conflicts between R packages, for example, the MethylSet object in wateRmelon and minfi are different because the one in minfi has been updated in the newest version while the wateRmelon still use the previous object constructor. It is should be noticed in case of using different version of them. […]
Placental CpG methylation of infants born extremely preterm predicts cognitive impairment later in life
[…] ed from analysis (n = 24,591), as recommended by the manufacturer. Subsequently, data were normalized using the beta-mixture quantile (BMIQ) normalization methodology []. This was performed using the wateRmelon package (version 1.11.0) in R (version 3.2.3; The R Project for Statistical Computing) []. Probes that represent known single nucleotide polymorphisms (SNPs) (n = 84,124) and probes that ar […]
Epigenetic Changes in the CRH Gene are Related to Severity of Suicide Attempt and a General Psychiatric Risk Score in Adolescents
[…] hite blood cell-type heterogeneity. Principal component analysis (PCA) was used to identify sample outliers in the methylation data. Methylation preprocessing steps were performed using the minfi (), watermelon (), sva (), ChAMP () and FactoMineR () packages of the Bioconductor project operable in R software, version 3.3.0. […]
Microorganisms in the human placenta are associated with altered CpG methylation of immune and inflammation related genes
[…] that had high detection P-values (P>0.1) were removed from analysis (n = 24,591). Following data filtration, data were normalized using the beta-mixture quantile (BMIQ) normalization method using the wateRmelon package (version 1.11.0) in R (version 3.2.3). After normalization, probes that were annotated as single nucleotide polymorphisms (SNPs) by Illumina were removed from further analysis (n = […]
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