bioc-issue-bot
commented
2 years ago Hi @daanhazelaar
Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.
The DESCRIPTION file for this package is:
Package: katdetectr
Title: Detection, Characterization and Visualization of Kataegis in Sequencing Data
Version: 0.99.0
Authors@R: c(
person("Daan", "Hazelaar", , "daanhazelaar@gmail.com", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-7513-6813")),
person("Job", "van Riet", , "j.vanriet@erasmusmc.nl", role = c("aut"),
comment = c(ORCID = "0000-0001-7767-7923")),
person("Harmen", "van de Werken", , "h.vandewerken@erasmusmc.nl", role = c("ths"),
comment = c(ORCID = "0000-0002-9794-1477"))
)
Description: Kataegis refers to the occurrence of regional hypermutation and is
a phenomenon observed in a wide range of malignancies. Using changepoint detection
katdetectr aims to identify putative kataegis foci from common data-formats housing genomic variants.
Katdetectr has shown to be a robust package for the detection, characterization and visualisation of kataegis.
License: GPL-3 + file LICENSE
URL: https://github.com/ErasmusMC-CCBC/katdetectr
BugReports: https://github.com/ErasmusMC-CCBC/katdetectr
Depends:
R (>= 4.1.0)
Imports:
base (>= 4.1.3),
BiocParallel (>= 1.26.2),
BiocStyle (>= 2.20.0),
changepoint (>= 2.2.3),
changepoint.np (>= 1.0.3),
checkmate (>= 2.0.0),
dplyr (>= 1.0.8),
GenomicRanges (>= 1.44.0),
GenomeInfoDb (>= 1.28.4),
IRanges (>= 2.26.0),
maftools (>= 2.10.5),
methods (>= 4.1.3),
rlang (>= 1.0.2),
S4Vectors (>= 0.30.2),
tibble (>= 3.1.6),
VariantAnnotation (>= 1.38.0),
Biobase (>= 2.54.0),
Rdpack (>= 2.3),
ggplot2 (>= 3.3.5),
tidyr (>= 1.2.0),
BSgenome (>= 1.62.0)
Suggests:
BSgenome.Hsapiens.UCSC.hg38 (>= 1.4.4),
ggtext (>= 0.1.1),
scales (>= 1.2.0),
knitr (>= 1.37),
rmarkdown (>= 2.13),
testthat (>= 3.0.0),
BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.3)
RdMacros: Rdpack
VignetteBuilder:
knitr
biocViews: WholeGenome, Software, SNP, Sequencing, Classification, VariantAnnotation
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.1.2
Config/testthat/edition: 3
vjcitn
daanhazelaar
lazappi
lshep
nturaga
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