mist
This is the development version of mist; to use it, please install the devel version of Bioconductor.
Differential Methylation Analysis for scDNAm Data
Bioconductor version: Development (3.21)
mist (Methylation Inference for Single-cell along Trajectory) is a hierarchical Bayesian framework for modeling DNA methylation trajectories and performing differential methylation (DM) analysis in single-cell DNA methylation (scDNAm) data. It estimates developmental-stage-specific variations, identifies genomic features with drastic changes along pseudotime, and, for two phenotypic groups, detects features with distinct temporal methylation patterns. mist uses Gibbs sampling to estimate parameters for temporal changes and stage-specific variations.
Author: Daoyu Duan [aut, cre] (ORCID:
Maintainer: Daoyu Duan <dxd429 at case.edu>
citation("mist")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("mist")
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("mist")| mist_vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DNAMethylation, DifferentialMethylation, Epigenetics, SingleCell, Software |
| Version | 0.99.17 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | BiocParallel, MCMCpack, Matrix, S4Vectors, methods, rtracklayer, car, mvtnorm, SummarizedExperiment, SingleCellExperiment, BiocGenerics, stats, rlang |
| System Requirements | |
| URL | https://https://github.com/dxd429/mist |
| Bug Reports | https://https://github.com/dxd429/mist/issues |
See More
| Suggests | knitr, rmarkdown, RUnit, ggplot2, 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 | mist_0.99.17.tar.gz |
| Windows Binary (x86_64) | mist_0.99.17.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/mist |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/mist |
| Bioc Package Browser | https://code.bioconductor.org/browse/mist/ |
| Package Short Url | https://bioconductor.org/packages/mist/ |
| Package Downloads Report | Download Stats |