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("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 |
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 |