epialleleR - Fast, Epiallele-Aware Methylation Caller and Reporter

Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Among other things, this package can also extract and visualise methylation patterns and assess allele specificity of methylation.

Last updated 1 days ago

dnamethylationepigeneticsmethylseqlongreadbioconductordna-methylationepiallelenext-generation-sequencingsamtools

6.02 score 4 stars 5 scripts 160 downloads

ExtDist - Extending the Range of Functions for Probability Distributions

A consistent, unified and extensible framework for estimation of parameters for probability distributions, including parameter estimation procedures that allow for weighted samples; the current set of distributions included are: the standard beta, The four-parameter beta, Burr, gamma, Gumbel, Johnson SB and SU, Laplace, logistic, normal, symmetric truncated normal, truncated normal, symmetric-reflected truncated beta, standard symmetric-reflected truncated beta, triangular, uniform, and Weibull distributions; decision criteria and selections based on these decision criteria.

Last updated 1 years ago

6.00 score 1 stars 3 packages 55 scripts 580 downloads

ramr - Detection of Rare Aberrantly Methylated Regions in Array and NGS Data

ramr is an R package for detection of low-frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. In addition, package provides functions to visualize found aberrantly methylated regions (AMRs), to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms.

Last updated 19 days ago

dnamethylationdifferentialmethylationepigeneticsmethylationarraymethylseqaberrant-methylationbioconductordna-methylationepimutationmethylation-microarraysnext-generation-sequencing

4.30 score 5 scripts 137 downloads