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MethScope identifies Most Recurrent Methylation Patterns (MRMPs) as the basis to encode latent representations for interpretatble analysis of DNA mehtylation data, in particular single cell and spatial methylome. The MRMPs embeddings will support automatic cell annotation, bulk deconvolution, unsupervisded clustering, and cancer cell of origin prediction.
MethScope requires R >= 4.0 and the zlib system library.
Install the released version of usethis from CRAN:
install.packages("MethScope")or install from github
devtools::install_github("zhou-lab/MethScope")MethScope performs rapid cell annotation, deconvolution and other tasks for single cell and spatial DNA methylome. Please check out our documentation for more details:
The CRAN package includes a small toy dataset for quick installation checks and examples:
qry <- system.file("extdata", "toy.cg", package = "MethScope")
msk <- system.file("extdata", "toy.cm", package = "MethScope")
res <- GenerateInput(qry, msk)The GitHub repository also provides a larger
inst/extdata/example.cg file for fuller end-to-end testing
after cloning the repository. This larger file is excluded from CRAN
builds to keep the package size appropriate for CRAN.
qry <- "inst/extdata/example.cg"
msk <- system.file("extdata", "toy.cm", package = "MethScope")
res <- GenerateInput(qry, msk)If you use MethScope, kindly cite (coming soon):
Hongxiang Fu, Chin Nien Lee, Cameron Cloud, Hao Xu, Yanxiang Deng, Wanding Zhou, MethScope: Ultra-fast Analysis of Sparse DNA Methylome via Recurrent Pattern Encoding.
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.