Package: vmrseq 1.5.0

Ning Shen

vmrseq: Probabilistic Modeling of Single-cell Methylation Heterogeneity

High-throughput single-cell measurements of DNA methylation allows studying inter-cellular epigenetic heterogeneity, but this task faces the challenges of sparsity and noise. We present vmrseq, a statistical method that overcomes these challenges and identifies variably methylated regions accurately and robustly.

Authors:Ning Shen [aut, cre]

vmrseq_1.5.0.tar.gz
vmrseq_1.5.0.zip(r-4.7)vmrseq_1.5.0.zip(r-4.6)vmrseq_1.5.0.zip(r-4.5)
vmrseq_1.5.0.tgz(r-4.6-any)vmrseq_1.5.0.tgz(r-4.5-any)
vmrseq_1.5.0.tar.gz(r-4.7-any)vmrseq_1.5.0.tar.gz(r-4.6-any)
vmrseq_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
vmrseq/json (API)

# Install 'vmrseq' in R:

install.packages('vmrseq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nshen7/vmrseq/issues

Datasets:

cell_1 - Cell_1
cell_2 - Cell_2
cell_3 - Cell_3
toy.gr - Toy.gr
toy.results - Toy.results

On BioConductor:vmrseq-1.5.0(bioc 3.24)vmrseq-1.4.0(bioc 3.23)

software immunooncology dnamethylation epigenetics singlecell sequencing wholegenome computational-biology dimensionality-reduction epigenomics-workflow hidden-markov-model probabilistic-models

5.18 score 10 stars 5 scripts 248 downloads 8 exports 181 dependencies

Last updated from:350bbc11e7. Checks:8 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	242
linux-devel-x86_64	NOTE	482
source / vignettes	OK	366
linux-release-x86_64	NOTE	438
macos-release-arm64	NOTE	392
macos-oldrel-arm64	NOTE	360
windows-devel	NOTE	422
windows-release	NOTE	443
windows-oldrel	NOTE	423
wasm-release	OK	191

Exports:HDF5NAdrop2matrix poolData regionSummary tpEstimate tpPlot vmrseqFit vmrseqOptimControl vmrseqSmooth

Dependencies:abind AnnotationDbi arules askpass base64enc BH Biobase BiocBaseUtils BiocGenerics BiocIO biocmake BiocParallel Biostrings bit bit64 bitops blob brew brio bslib bumphunter cachem callr cigarillo cli clipr codetools commonmark cpp11 crayon credentials curl data.table DBI DelayedArray desc devtools diffobj digest dir.expiry doRNG downlit dplyr ellipsis evaluate fansi farver fastmap filelock float fontawesome foreach formatR fs futile.logger futile.options gamlss.dist generics GenomicAlignments GenomicFeatures GenomicRanges gert ggplot2 gitcreds glue gtable h5mread HDF5Array highr htmltools htmlwidgets httpuv httr httr2 ini IRanges irlba isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mime miniUI openssl otel pak pillar pkgbuild pkgconfig pkgdown pkgload png praise prettyunits processx profvis promises proxy ps purrr R6 ragg rappdirs rcmdcheck RColorBrewer Rcpp RcppProgress RCurl recommenderlab recosystem registry restfulr rhdf5 rhdf5filters Rhdf5lib Rhtslib rjson rlang rmarkdown rngtools roxygen2 rprojroot Rsamtools RSQLite rstudioapi rtracklayer rversions S4Arrays S4Vectors S7 sass scales Seqinfo sessioninfo shiny snow sourcetools SparseArray statmod stringi stringr SummarizedExperiment sys systemfonts testthat textshaping tibble tidyr tidyselect tinytex urlchecker usethis utf8 vctrs viridisLite waldo whisker withr xfun XML xml2 xopen xtable XVector yaml zip

Analyzing single-cell bisulfite sequencing data with vmrseq

Rendered fromvmrseq-vignette.Rmdusingknitr::rmarkdown

Last update: 2025-04-30
Started: 2023-05-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
cell_1	cell_1
cell_2	cell_2
cell_3	cell_3
Coerce a NA-dropped HDF5 matrix back to regular matrix form where NAs are not dropped to 0.	HDF5NAdrop2matrix
Pool single-cell file together into an HDF5-based SummarizedExperiment object with sparse matrix representation.	poolData
Compute regional methylation information for individual cells.	regionSummary
toy.gr	toy.gr
toy.results	toy.results
Estimate transition probilities conditioning on CpG-CpG distance	tpEstimate
Plot transition probability distribution	tpPlot
Construct candidate regions and detect variably methylated regions.	vmrseqFit
Auxiliary function as user interface for vmrseq optimization.	vmrseqOptimControl
Smoothing on single-cell bisulfite sequencing data for the purpose of constructing candidate regions.	vmrseqSmooth