wateRmelon statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

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)
library_books

Impact on birth weight of maternal smoking throughout pregnancy mediated by DNA methylation

2018
BMC Genomics
PMCID: 5922319
PMID: 29695247
DOI: 10.1186/s12864-018-4652-7

[…] 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 []. […]

library_books

Epigenome Wide Association Study of Soluble Tumor Necrosis Factor Receptor 2 Levels in the Framingham Heart Study

2018
Front Pharmacol
PMCID: 5928448
PMID: 29740313
DOI: 10.3389/fphar.2018.00207

[…] 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- […]

library_books

A framework for analyzing DNA methylation data from Illumina Infinium HumanMethylation450 BeadChip

2018
BMC Bioinformatics
PMCID: 5907140
PMID: 29671397
DOI: 10.1186/s12859-018-2096-3

[…] 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. […]

library_books

Placental CpG methylation of infants born extremely preterm predicts cognitive impairment later in life

2018
PLoS One
PMCID: 5841757
PMID: 29513726
DOI: 10.1371/journal.pone.0193271

[…] 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 […]

library_books

Epigenetic Changes in the CRH Gene are Related to Severity of Suicide Attempt and a General Psychiatric Risk Score in Adolescents

2017
PMCID: 5828554
PMID: 29277323
DOI: 10.1016/j.ebiom.2017.12.018

[…] 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. […]

library_books

Microorganisms in the human placenta are associated with altered CpG methylation of immune and inflammation related genes

2017
PLoS One
PMCID: 5730116
PMID: 29240761
DOI: 10.1371/journal.pone.0188664

[…] 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 = […]

Citations

Looking to check out a full list of citations?

wateRmelon institution(s)
Social, Genetic and Developmental Psychiatry, Institute of Psychiatry, King's College London, De Crespigny Park, London, UK

wateRmelon reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review wateRmelon