methVisual: Methods for visualization and statistics on DNA methylation data
Version 1.28.0

The package 'methVisual' allows the visualization of DNA methylation data after bisulfite sequencing.

Browse man pages Browse package API and functions Browse package files

AuthorA. Zackay, C. Steinhoff
Bioconductor views Classification Clustering DNAMethylation
Date of publicationNone
MaintainerArie Zackay <arie.zackay@mail.huji.ac.il>
LicenseGPL (>= 2)
Version1.28.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("methVisual")

Man pages

cgInAlign: Amount of CpGs
cgMethFinder: Methylation status
Cooccurrence: Visualization of binary methylation data
coversionGenom: Sequence conversion
findNonAligned: Aligned CpG positions
heatMapMeth: HeatMap diagram over methylation data
makeDataMethGFF: GFF methylation files
makeLocalExpDir: Saving example data
makeTabFilePath: Tab delimited text file
matrixSNP: Correlation between methylation states
MethAlignNW: Summary of methylation states
methCA: CA on methylation
methData: BiQAnalyzer dataset
MethDataInput: Sequences match control
methFisherTest: Fisher exact Test on methylation Data
MethLollipops: "Lollipops" Methylation plot
methWhitneyUTest: Mann Whitney U-Test on methylation data
MethylQC: Quality controle (QC) on Methylation Data
plotAbsMethyl: Plot number mathylation on CpGs positions
plotMatrixSNP: Plot of methylation states dependencies
readBisulfFASTA: Read multiple FASTA file
selectRefSeq: Uploading genomic sequence

Functions

Cooccurrence Man page Source code
MethAlignNW Man page Source code
MethDataInput Man page Source code
MethLollipops Man page Source code
MethylQC Man page Source code
cgInAlign Man page Source code
cgMethFinder Man page Source code
coversionGenom Man page Source code
findNonAligned Man page Source code
heatMapMeth Man page Source code
makeDataMethGFF Man page Source code
makeLocalExpDir Man page Source code
makeTabFilePath Man page Source code
matrixSNP Man page Source code
methCA Man page Source code
methData Man page
methFisherTest Man page Source code
methWhitneyUTest Man page Source code
plotAbsMethyl Man page Source code
plotMatrixSNP Man page Source code
readBisulfFASTA Man page Source code
selectRefSeq Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/MethAlignNW.R
R/MethDataInput.R
R/MethVisual.R
R/MethylQC.R
build
build/vignette.rds
data
data/methData.RData
inst
inst/doc
inst/doc/methVisual.R
inst/doc/methVisual.Rnw
inst/doc/methVisual.pdf
inst/examples
inst/examples/BiqAnalyzer
inst/examples/BiqAnalyzer/Demo_data
inst/examples/BiqAnalyzer/Demo_data/seq_A.fasta
inst/examples/BiqAnalyzer/Demo_data/seq_B.fasta
inst/examples/BiqAnalyzer/Demo_data/seq_C.fasta
inst/examples/BiqAnalyzer/Demo_data/seq_D.fasta
inst/examples/BiqAnalyzer/Demo_data/seq_E.fasta
inst/examples/BiqAnalyzer/Demo_data/seq_F.fasta
inst/examples/BiqAnalyzer/Demo_data/seq_G.fasta
inst/examples/BiqAnalyzer/Demo_data/seq_H.fasta
inst/examples/BiqAnalyzer/Demo_data/seq_I.fasta
inst/examples/BiqAnalyzer/Demo_data/seq_J.fasta
inst/examples/BiqAnalyzer/Master_Sequence.txt
inst/examples/BiqAnalyzer/multiFASTA.fasta
inst/examples/GFF
inst/examples/GFF/1.gff
inst/examples/GFF/2.gff
inst/examples/GFF/3.gff
inst/examples/GFF/4.gff
inst/examples/GFF/5.gff
man
man/Cooccurrence.Rd
man/MethAlignNW.Rd
man/MethDataInput.Rd
man/MethLollipops.Rd
man/MethylQC.Rd
man/cgInAlign.Rd
man/cgMethFinder.Rd
man/coversionGenom.Rd
man/findNonAligned.Rd
man/heatMapMeth.Rd
man/makeDataMethGFF.Rd
man/makeLocalExpDir.Rd
man/makeTabFilePath.Rd
man/matrixSNP.Rd
man/methCA.Rd
man/methData.Rd
man/methFisherTest.Rd
man/methWhitneyUTest.Rd
man/plotAbsMethyl.Rd
man/plotMatrixSNP.Rd
man/readBisulfFASTA.Rd
man/selectRefSeq.Rd
vignettes
vignettes/methVisual.Rnw
methVisual documentation built on May 20, 2017, 10:22 p.m.