Welcome to the new bioconductor.org!

DMCFB

Differentially Methylated Cytosines via a Bayesian Functional Approach


Bioconductor version: Release (3.18)

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 [aut, cre]

Maintainer: Farhad Shokoohi <shokoohi at icloud.com>

Citation (from within R, enter citation("DMCFB")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
Identifying DMCs using Bayesian functional regressions in BS-Seq data HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Bayesian, Coverage, DifferentialMethylation, Regression, Sequencing, Software
Version 1.16.1
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License GPL-3
Depends R (>= 4.3.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges
Imports utils, stats, speedglm, MASS, data.table, splines, arm, rtracklayer, benchmarkme, tibble, matrixStats, fastDummies, graphics
System Requirements
URL
Bug Reports https://github.com/shokoohi/DMCFB/issues
See More
Suggests testthat, knitr, rmarkdown, BiocStyle
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package DMCFB_1.16.1.tar.gz
Windows Binary DMCFB_1.16.1.zip (64-bit only)
macOS Binary (x86_64) DMCFB_1.16.1.tgz
macOS Binary (arm64) DMCFB_1.16.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/DMCFB
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/DMCFB
Bioc Package Browser https://code.bioconductor.org/browse/DMCFB/
Package Short Url https://bioconductor.org/packages/DMCFB/
Package Downloads Report Download Stats