MethTargetedNGS: Perform Methylation Analysis on Next Generation Sequencing Data

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

Author
Muhammad Ahmer Jamil with Contribution of Prof. Holger Frohlich and Priv.-Doz. Dr. Osman El-Maarri
Date of publication
None
Maintainer
Muhammad Ahmer Jamil <engr.ahmerjamil@gmail.com>
License
Artistic-2.0
Version
1.6.0

View on Bioconductor

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)

Files in this package

MethTargetedNGS/DESCRIPTION
MethTargetedNGS/NAMESPACE
MethTargetedNGS/R
MethTargetedNGS/R/bisulfiteConversion.R
MethTargetedNGS/R/hmmer.R
MethTargetedNGS/R/sequenceAlignment.R
MethTargetedNGS/build
MethTargetedNGS/build/vignette.rds
MethTargetedNGS/inst
MethTargetedNGS/inst/doc
MethTargetedNGS/inst/doc/MethTargetedNGS.R
MethTargetedNGS/inst/doc/MethTargetedNGS.Rnw
MethTargetedNGS/inst/doc/MethTargetedNGS.pdf
MethTargetedNGS/inst/extdata
MethTargetedNGS/inst/extdata/Healthy.fasta
MethTargetedNGS/inst/extdata/Reference.fasta
MethTargetedNGS/inst/extdata/Tumor.fasta
MethTargetedNGS/inst/extdata/bisulfite.fasta
MethTargetedNGS/inst/extdata/msa.fasta
MethTargetedNGS/man
MethTargetedNGS/man/MethTargetedNGS-package.Rd
MethTargetedNGS/man/bconv.Rd
MethTargetedNGS/man/compare_samples.Rd
MethTargetedNGS/man/fishertest_cpg.Rd
MethTargetedNGS/man/hmmbuild.Rd
MethTargetedNGS/man/methAlign.Rd
MethTargetedNGS/man/methAvg.Rd
MethTargetedNGS/man/methEntropy.Rd
MethTargetedNGS/man/methHeatmap.Rd
MethTargetedNGS/man/nhmmer.Rd
MethTargetedNGS/man/odd_ratio.Rd
MethTargetedNGS/vignettes
MethTargetedNGS/vignettes/MethTargetedNGS.Rnw