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vmrseq

An R package for detecting cell-to-cell variably methylated regions (VMRs) from single-cell bisulfite sequencing leveraging probabilistic models.

https://github.com/nshen7/vmrseq

Science Score: 49.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
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    Committers with academic emails
    1 of 7 committers (14.3%) from academic institutions
  • ○
    Institutional organization owner
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (12.2%) to scientific vocabulary

Keywords

computational-biology dimensionality-reduction epigenomics-workflow hidden-markov-model probabilistic-models r-package
Last synced: 6 months ago · JSON representation

Repository

An R package for detecting cell-to-cell variably methylated regions (VMRs) from single-cell bisulfite sequencing leveraging probabilistic models.

Basic Info
  • Host: GitHub
  • Owner: nshen7
  • License: mit
  • Language: R
  • Default Branch: main
  • Homepage:
  • Size: 85.9 MB
Statistics
  • Stars: 9
  • Watchers: 0
  • Forks: 0
  • Open Issues: 0
  • Releases: 3
Topics
computational-biology dimensionality-reduction epigenomics-workflow hidden-markov-model probabilistic-models r-package
Created over 3 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License

README.md

Example Image

vmrseq: Detecting variably methylated regions (VMRs) from single-cell bisulfite sequencing

The R package vmrseq is a novel computational tool developed for pinpointing variably methylated regions (VMRs) in scBS-seq data without prior knowledge on size or location. High-throughput single-cell measurements of DNA methylation allows studying inter-cellular epigenetic heterogeneity, but this task faces the challenges of sparsity and noise. vmrseq overcomes these challenges and identifies variably methylated regions accurately and robustly.

Method Figure

Installation

You can install the development version of vmrseq in R from Bioconductor (recommended) or GitHub with:

``` r

Install stable version from Bioconductor

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("vmrseq")

Or development version from Github

install.packages("remotes")

remotes::install_github("nshen7/vmrseq") ```

Online Vignette

Docker Image

We provide a Docker image for robust setup and use of this package. The Docker image includes all necessary dependencies for the package and vignettes. To pull the Docker image from Docker Hub, use the following command in bash:

bash docker pull nshen7/vmrseq-bioc-3.19:latest

Citation

Shen, N., Korthauer, K. vmrseq: probabilistic modeling of single-cell methylation heterogeneity. Genome Biol 25, 321 (2024). https://doi.org/10.1186/s13059-024-03457-7

License/Copyright

License: MIT This package is made available under an MIT license.

Owner

  • Name: Ning Shen
  • Login: nshen7
  • Kind: user

GitHub Events

Total
  • Issues event: 1
  • Watch event: 2
  • Delete event: 2
  • Push event: 15
  • Pull request event: 10
  • Create event: 5
Last Year
  • Issues event: 1
  • Watch event: 2
  • Delete event: 2
  • Push event: 15
  • Pull request event: 10
  • Create event: 5

Committers

Last synced: 6 months ago

All Time
  • Total Commits: 172
  • Total Committers: 7
  • Avg Commits per committer: 24.571
  • Development Distribution Score (DDS): 0.122
Past Year
  • Commits: 15
  • Committers: 2
  • Avg Commits per committer: 7.5
  • Development Distribution Score (DDS): 0.333
Top Committers
Name Email Commits
NingShen1997 s****7@g****m 151
Ning Shen 3****7@u****m 10
Ning Shen n****7@s****e 4
Ning Shen sn@N****l 3
Ning Shen sn@d****a 2
Ning Shen n****7@s****e 1
Ning Shen n****7@s****e 1
Committer Domains (Top 20 + Academic)
se228.ib.sockeye: 1 se081.ib.sockeye: 1 dhcp-206-12-45-148.ubcsecure.wireless.ubc.ca: 1 se094.ib.sockeye: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 1
  • Total pull requests: 14
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 13
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 7
  • Average time to close issues: N/A
  • Average time to close pull requests: less than a minute
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 6
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • olaraym (1)
Pull Request Authors
  • nshen7 (15)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 903 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 2
  • Total maintainers: 1
bioconductor.org: vmrseq

Probabilistic Modeling of Single-cell Methylation Heterogeneity

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 903 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 30.3%
Average: 41.5%
Downloads: 94.2%
Maintainers (1)
ning.shen.wk@gmail.com
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 2.10 depends
  • BiocParallel * imports
  • GenomicRanges * imports
  • bumphunter * imports
  • dplyr * imports
  • ggplot2 * imports