Introduction | Installation | Example Workflow for Single-Group Analysis | Step 1: Load Example Data | Step 2: Estimate Parameters Using estiParam | Step 3: Perform Differential Methylation Analysis Using dmSingle | Step 4: Perform Differential Methylation Analysis Using plotGene | Example Workflow for Two-Group Analysis | Step 1: Load Two-Group Data | Step 3: Perform Differential Methylation Analysis for Two-Group Comparison Using dmTwoGroups | Conclusion | Session info
Package: mist 1.5.0
Daoyu Duan
mist: Differential Methylation Analysis for scDNAm Data
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.
Authors:
mist_1.5.0.tar.gz
mist_1.5.0.zip(r-4.7)mist_1.5.0.zip(r-4.6)mist_1.5.0.zip(r-4.5)
mist_1.5.0.tgz(r-4.6-any)mist_1.5.0.tgz(r-4.5-any)
mist_1.5.0.tar.gz(r-4.7-any)mist_1.5.0.tar.gz(r-4.6-any)
mist_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
mist/json (API)
| # Install 'mist' in R: |
| install.packages('mist', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dxd429/mist/issues
On BioConductor:mist-1.5.0(bioc 3.24)mist-1.4.0(bioc 3.23)
epigeneticsdifferentialmethylationdnamethylationsinglecellsoftware
Last updated from:8e21d2e7c0. Checks:1 NOTE, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 207 | ||
| linux-devel-x86_64 | OK | 403 | ||
| source / vignettes | OK | 333 | ||
| linux-release-x86_64 | OK | 486 | ||
| macos-release-arm64 | OK | 229 | ||
| macos-oldrel-arm64 | OK | 225 | ||
| windows-devel | OK | 428 | ||
| windows-release | OK | 422 | ||
| windows-oldrel | OK | 427 | ||
| wasm-release | OK | 196 |
Exports:dmSingledmTwoGroupsestiParamplotGene
Dependencies:abindaskpassbackportsBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopsbootbroomcarcarDatacigarilloclicodacodetoolscolorspacecowplotcpp11crayoncurlDelayedArrayDerivdoBydplyrfarverforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesggplot2gluegtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmcmcMCMCpackmgcvmimeminqamodelrmvtnormnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigpurrrquantregR6rbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreformulasrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4ArraysS4VectorsS7scalesSeqinfoSingleCellExperimentsnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewithrXMLXVectoryamlzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Differential methylation evaluation over time for scDNA-seq data under the 1-group scenario. | dmSingle |
| Differential methylation evaluation over time for scDNA-seq data under the 2-group scenario. | dmTwoGroups |
| Parameter Estimation With mist | estiParam |
| Plot Methylation Levels vs. Pseudotime for a Specific Gene | plotGene |
| Small Sample Single-Cell Data for Testing and Illustration | small_sampleData_sce_g1 |
| Small Sample Single-Cell Data for Testing and Illustration | small_sampleData_sce_g2 |
