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DESCRIPTION
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DESCRIPTION
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Package: scMethrix
Title: Fast and efficient summarization of single cell whole genome bisulfate data
Version: 0.1.0.0002
Authors@R:
person("Lindsay","Andrew", role = c("aut", "cre"), email = "a.lindsay@dkfz.de", comment = c(ORCID = "0000-0001-6607-5812"))
Description: This package summarizes single cell bisulfite data as stored in bedgraph files generated from multiple upstream pipelines. Available functions include: subsetting, filtering, imputing, clustering, and binning. Summarized data can be exported in multiple formats.
License: Apache License (>= 2)
Encoding: UTF-8
LazyData: false
Depends: R (>= 3.6), data.table (>= 1.12.4), SingleCellExperiment
Imports:
rtracklayer,
DelayedArray,
HDF5Array,
DelayedMatrixStats,
parallel,
methods,
matrixStats,
tools,
graphics,
stats,
utils,
GenomicRanges,
IRanges,
SummarizedExperiment,
doParallel,
GenomeInfoDb,
methrix,
umap,
ggplot2,
BPRMeth,
RColorBrewer,
Melissa,
missMDA,
Rtsne,
missForest,
impute,
SimDesign,
Metrics,
bioDist,
mclust,
bsseq,
Seurat,
S4Vectors,
BSgenome,
Biostrings
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Suggests:
rmarkdown,
testthat,
knitr,
BSgenome.Mmusculus.UCSC.mm10,
BiocManager,
R.utils
URL: https://github.com/CompEpigen/scMethrix
BugReports: https://github.com/CompEpigen/scMethrix/issues
biocViews: DNAMethylation, Sequencing, Coverage
VignetteBuilder: knitr