methVisual: Methods for visualization and statistics on DNA methylation data

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

Author
A. Zackay, C. Steinhoff
Date of publication
None
Maintainer
Arie Zackay <arie.zackay@mail.huji.ac.il>
License
GPL (>= 2)
Version
1.26.0

View on Bioconductor

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

Files in this package

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