mist
This is thereleased version of mist; for the devel version, seemist.
Differential Methylation Analysis for scDNAm Data
Bioconductor version: Release (3.22)
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: 0000-0002-3147-2006
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")BiocManager::install("mist")For older versions of R, please refer to the appropriateBioconductor 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 | 1.2.0 |
| In Bioconductor since | BioC 3.21 (R-4.5) (0.5 years) |
| License | MIT + fileLICENSE |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | mist_1.2.0.tar.gz |
| Windows Binary (x86_64) | mist_1.2.0.zip |
| macOS Binary (x86_64) | mist_1.2.0.tgz |
| macOS Binary (arm64) | mist_1.2.0.tgz |
| 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 |