DMCFB

DOI: 10.18129/B9.bioc.DMCFB    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see DMCFB.

Differentially Methylated Cytosines via a Bayesian Functional Approach

Bioconductor version: 3.11

DMCFB is a pipeline for identifying differentially methylated cytosines using a Bayesian functional regression model in bisulfite sequencing data. By using a functional regression data model, it tries to capture position-specific, group-specific and other covariates-specific methylation patterns as well as spatial correlation patterns and unknown underlying models of methylation data. It is robust and flexible with respect to the true underlying models and inclusion of any covariates, and the missing values are imputed using spatial correlation between positions and samples. A Bayesian approach is adopted for estimation and inference in the proposed method.

Author: Farhad Shokoohi

Maintainer: Farhad Shokoohi <shokoohi at icloud.com>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DMCFB")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("DMCFB")

 

HTML	R Script	Identifying DMCs using Bayesian functional regressions in BS-Seq data
PDF		Reference Manual
Text		NEWS

Details

biocViews	Bayesian, Coverage, DifferentialMethylation, Regression, Sequencing, Software
Version	1.2.0
In Bioconductor since	BioC 3.10 (R-3.6) (1 year)
License	GPL-3
Depends	R (>= 3.6.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges
Imports	utils, stats, speedglm, MASS, data.table, splines, arm, rtracklayer, benchmarkme, tibble, matrixStats, fastDummies, graphics
LinkingTo
Suggests	testthat, knitr, rmarkdown
SystemRequirements
Enhances
URL
BugReports	https://github.com/shokoohi/DMCFB/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	DMCFB_1.2.0.tar.gz
Windows Binary	DMCFB_1.2.0.zip
macOS 10.13 (High Sierra)	DMCFB_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DMCFB
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DMCFB
Package Short Url	https://bioconductor.org/packages/DMCFB/
Package Downloads Report	Download Stats