https://github.com/bioconductor-source/vmrseq
Science Score: 26.0%
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
-
✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
-
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (11.7%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: bioconductor-source
- License: mit
- Language: R
- Default Branch: devel
- Size: 85.6 MB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
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.
Installation
You can install the development version of vmrseq in R from
GitHub with:
``` r
install.packages("devtools")
devtools::install_github("nshen7/vmrseq") ```
Online Vignette
- An online vignette of 'Get Started' on the
vmrseqpackage can be found at https://rpubs.com/nshen7/vmrseq-vignette. - An example workflow on scBS-seq data analysis using
vmrseqcan be found at https://github.com/nshen7/vmrseq-workflow-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
Ning Shen and Keegan Korthauer. 2023. “Vmrseq: Probabilistic Modeling of Single-Cell Methylation Heterogeneity.” bioRxiv. https://doi.org/10.1101/2023.11.20.567911.
License/Copyright
This package is made available under an MIT license.
Owner
- Name: (WIP DEV) Bioconductor Packages
- Login: bioconductor-source
- Kind: organization
- Email: maintainer@bioconductor.org
- Website: https://bioconductor.org
- Repositories: 1
- Profile: https://github.com/bioconductor-source
Source code for packages accepted into Bioconductor
GitHub Events
Total
Last Year
Dependencies
- JamesIves/github-pages-deploy-action v4.5.0 composite
- actions/checkout v4 composite
- r-lib/actions/setup-pandoc v2 composite
- r-lib/actions/setup-r v2 composite
- r-lib/actions/setup-r-dependencies v2 composite
- R >= 3.5.0 depends
- BiocParallel * imports
- DelayedArray * imports
- GenomicRanges * imports
- HDF5Array * imports
- IRanges * imports
- S4Vectors * imports
- SummarizedExperiment * imports
- bumphunter * imports
- data.table * imports
- dplyr * imports
- gamlss.dist * imports
- ggplot2 * imports
- locfit * imports
- methods * imports
- recommenderlab * imports
- tidyr * imports
- knitr * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests