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DESCRIPTION
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DESCRIPTION
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Package: NanoMethViz
Type: Package
Title: Visualise methylation data from Oxford Nanopore sequencing
Version: 3.1.5
Authors@R: c(
person("Shian", "Su", email = "su.s@wehi.edu.au", role = c("cre", "aut")))
Description: NanoMethViz is a toolkit for visualising methylation data from
Oxford Nanopore sequencing. It can be used to explore methylation patterns
from reads derived from Oxford Nanopore direct DNA sequencing with
methylation called by callers including nanopolish, f5c and megalodon. The
plots in this package allow the visualisation of methylation profiles
aggregated over experimental groups and across classes of genomic features.
biocViews:
Software,
LongRead,
Visualization,
DifferentialMethylation,
DNAMethylation,
Epigenetics,
DataImport
URL: https://github.com/shians/NanoMethViz
BugReports: https://github.com/Shians/NanoMethViz/issues
Depends:
R (>= 4.0.0),
methods,
ggplot2 (>= 3.4.0)
Imports:
cpp11 (>= 0.2.5),
readr,
cli,
S4Vectors,
SummarizedExperiment,
BiocSingular,
bsseq,
forcats,
assertthat,
AnnotationDbi,
Rcpp,
dplyr,
dbscan,
e1071,
fs,
GenomicRanges,
Biostrings,
ggrastr,
glue,
graphics,
IRanges,
limma (>= 3.44.0),
patchwork,
purrr,
rlang,
R.utils,
Rsamtools,
scales (>= 1.2.0),
stats,
stringr,
tibble,
tidyr,
utils,
withr,
zlibbioc
Suggests:
BiocStyle,
DSS,
Mus.musculus (>= 1.3.1),
Homo.sapiens (>= 1.3.1),
org.Hs.eg.db,
TxDb.Hsapiens.UCSC.hg19.knownGene,
TxDb.Hsapiens.UCSC.hg38.knownGene,
org.Mm.eg.db,
TxDb.Mmusculus.UCSC.mm10.knownGene,
TxDb.Mmusculus.UCSC.mm39.refGene,
knitr,
rmarkdown,
rtracklayer,
testthat (>= 3.0.0),
covr
LinkingTo: Rcpp
License: Apache License (>= 2.0)
SystemRequirements: C++20
VignetteBuilder: knitr
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Config/testthat/parallel: true
Config/testthat/edition: 3