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DESCRIPTION
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DESCRIPTION
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Package: INCOMMON
Title: Inference of copy number and mutation multiplicity in oncology
Version: 0.0.1
Author: Nicola Calonaci
Maintainer: Nicola Calonaci <[email protected]>
Authors@R:
c(person("Nicola", "Calonaci", , "[email protected]", role = c("aut", "cre"),
comment = c(ORCID = "0000-0003-2721-4888")),
person("Giulio", "Caravagna", , "[email protected]", role = c("aut", "cre"),
comment = c(ORCID = "")))
Description: INCOMMON is a tool for the INference of COpy number and Mutation Multiplicity in ONcology.
INCOMMON infers the copy number and multiplicity of somatic mutations from tumour-only read count data,
and can be applied to classify mutations from large-size datasets in an efficient and fast way.
Mutations are classified as either Tier-1 (present in 100% cells) without copy-number alterations
(heterozygous mutant diploid HMD), with loss of heterozygosity (LOH), copy-neutral LOH (CNLOH), amplification (AM),
or Tier-2 (subclonal or with high ploidy and low multiplicity).
License: GPL (>= 3)
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.1
Suggests:
knitr,
rmarkdown,
DT
Imports:
cli,
crayon,
ggplot2,
ggpubr,
CNAqc,
dplyr,
VGAM,
scales,
stats,
survival,
survminer,
patchwork,
ggrepel,
parallel,
purrr
Remotes:
caravagnalab/BMix,
caravagnalab/CNAqc
URL: https://github.com/caravagnalab/INCOMMON
BugReports: https://github.com/caravagnalab/INCOMMON/issues
VignetteBuilder: knitr
Depends:
R (>= 2.10)
LazyData: true