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MethTargetedNGS (version 1.4.0)

Perform Methylation Analysis on Next Generation Sequencing Data

Description

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

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Version

Version

1.4.0

License

Artistic-2.0

Maintainer

Muhammad Ahmer Jamil

Last Published

February 15th, 2017

Functions in MethTargetedNGS (1.4.0)

bconv

Convert non-bisulfite sequences to bisulfite sequences.
methHeatmap

Generate Heatmap of the given methylation data.
odd_ratio

Calculate log odd ratio of the given samples (healthy/tumor)
methEntropy

Calculate Methylation Entropy
methAvg

Calculate Methylation Average of given methylation matrix
MethTargetedNGS-package

Methylation Analysis of Next Generation Sequencing data.
methAlign

Align sequences with the reference sequence using pairwiseAlignment function from BioStrings
fishertest_cpg

Perform Fisher Exact Test on Methylation Data.
nhmmer

Calculate likelihood of the given profile hidden markov model against group of sequences
hmmbuild

Create Profile Hidden Markov Model of given aligned sequences
compare_samples

Complete Methylation Analysis of Next Generation Sequencing Data