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

Install the latest version of this package by entering the following in R:

```
source("https://bioconductor.org/biocLite.R")
biocLite("MethTargetedNGS")
```

Author | Muhammad 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 publication | None |

Maintainer | Muhammad Ahmer Jamil <engr.ahmerjamil@gmail.com> |

License | Artistic-2.0 |

Version | 1.6.0 |

**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)

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

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.

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