MethTargetedNGS: Perform Methylation Analysis on Next Generation Sequencing Data
Version 1.8.0

Perform step by step methylation analysis of Next Generation Sequencing data.

Browse man pages Browse package API and functions Browse package files

AuthorMuhammad Ahmer Jamil with Contribution of Prof. Holger Frohlich and Priv.-Doz. Dr. Osman El-Maarri
Bioconductor views Alignment DataImport Genetics ResearchField SequenceMatching Sequencing
Date of publicationNone
MaintainerMuhammad Ahmer Jamil <engr.ahmerjamil@gmail.com>
LicenseArtistic-2.0
Version1.8.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("MethTargetedNGS")

Man pages

bconv: Convert non-bisulfite sequences to bisulfite sequences.
compare_samples: Complete Methylation Analysis of Next Generation Sequencing...
fishertest_cpg: Perform Fisher Exact Test on Methylation Data.
hmmbuild: Create Profile Hidden Markov Model of given aligned sequences
methAlign: Align sequences with the reference sequence using...
methAvg: Calculate Methylation Average of given methylation matrix
methEntropy: Calculate Methylation Entropy
methHeatmap: Generate Heatmap of the given methylation data.
MethTargetedNGS-package: Methylation Analysis of Next Generation Sequencing data.
nhmmer: Calculate likelihood of the given profile hidden markov model...
odd_ratio: Calculate log odd ratio of the given samples (healthy/tumor)

Functions

MethTargetedNGS Man page
MethTargetedNGS-package Man page
bconv Man page Source code
compare_samples Man page Source code
fishertest_cpg Man page Source code
hmmbuild Man page Source code
methAlign Man page Source code
methAvg Man page Source code
methEntropy Man page Source code
methHeatmap Man page Source code
nhmmer Man page Source code
odd_ratio Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/bisulfiteConversion.R
R/hmmer.R
R/sequenceAlignment.R
build
build/vignette.rds
inst
inst/doc
inst/doc/MethTargetedNGS.R
inst/doc/MethTargetedNGS.Rnw
inst/doc/MethTargetedNGS.pdf
inst/extdata
inst/extdata/Healthy.fasta
inst/extdata/Reference.fasta
inst/extdata/Tumor.fasta
inst/extdata/bisulfite.fasta
inst/extdata/msa.fasta
man
man/MethTargetedNGS-package.Rd
man/bconv.Rd
man/compare_samples.Rd
man/fishertest_cpg.Rd
man/hmmbuild.Rd
man/methAlign.Rd
man/methAvg.Rd
man/methEntropy.Rd
man/methHeatmap.Rd
man/nhmmer.Rd
man/odd_ratio.Rd
vignettes
vignettes/MethTargetedNGS.Rnw
MethTargetedNGS documentation built on May 20, 2017, 9:20 p.m.