DMCFB
This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DMCFB.
Differentially Methylated Cytosines via a Bayesian Functional Approach
Bioconductor version: 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("DMCFB")):
Installation
To install this package, start R (version "3.6") 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 | ||
| NEWS | Text |
Details
| biocViews | Bayesian, Coverage, DifferentialMethylation, Regression, Sequencing, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (4.5 years) |
| 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 |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/shokoohi/DMCFB/issues |
See More
| Suggests | testthat, knitr, rmarkdown |
| 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_1.0.0.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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/DMCFB/ |
| Package Short Url | https://bioconductor.org/packages/DMCFB/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.10 | Source Archive |