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 |

**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)

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

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