DMCFB

DOI: 10.18129/B9.bioc.DMCFB    

Differentially Methylated Cytosines via a Bayesian Functional Approach

Bioconductor version: Release (3.10)

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>

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

Installation

To install this package, start R (version "3.6") 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 1.0.0
In Bioconductor since BioC 3.10 (R-3.6) (< 6 months)
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_1.0.0.tar.gz
Windows Binary DMCFB_1.0.0.zip
Mac OS X 10.11 (El Capitan) DMCFB_1.0.0.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/
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