This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

DMCFB

This is the development version of DMCFB; for the stable release version, see DMCFB.

Differentially Methylated Cytosines via a Bayesian Functional Approach

Bioconductor version: Development (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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("DMCFB")

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

Documentation

Reference Manual PDF

Details

biocViews Bayesian, Coverage, DifferentialMethylation, Regression, Sequencing, Software
Version 1.15.0
In Bioconductor since BioC 3.10 (R-3.6) (4 years)
License GPL-3
Depends R (>= 4.0.0), SummarizedExperiment, methods, S4Vectors, BiocParallel, GenomicRanges, IRanges
Imports utils, stats, speedglm, MASS, data.table, splines, arm, rtracklayer, benchmarkme, tibble, matrixStats, fastDummies, graphics
Linking To
Suggests testthat, knitr, rmarkdown
System Requirements
Enhances
URL
Bug Reports https://github.com/shokoohi/DMCFB/issues
See More
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
Windows Binary DMCFB_1.15.0.zip
macOS Binary (x86_64) DMCFB_1.15.0.tgz
macOS Binary (arm64) DMCFB_1.15.0.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