bioc-issue-bot
commented
3 months ago Hi @pliu55
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: MPAC
Title: Multi-omic Pathway Analysis of Cancer
Version: 0.99.0
Authors@R: c(
person(given="Peng", family="Liu", email="pliu55.wisc@gmail.com",
role = c("aut", "cre"), comment=c(ORCID="0000-0001-5655-2259")),
person(given="Paul", family="Ahlquist", role = c("aut")),
person(given="Anthony", family="Gitter", role = c("aut")),
person(given="Irene", family="Ong", role = c("aut")))
Description: Multi-omic Pathway Analysis of Cancer (MPAC), integrates
multi-omic data for understanding cancer mechanisms. It
predicts novel patient groups with distinct pathway profiles
as well as identifying key pathway proteins with potential clinical
associations. From CNA and RNA-seq data, it determines genes’ DNA and RNA
states (i.e., repressed, normal, or activated), which serve as the input
for PARADIGM to calculate Inferred Pathway Levels (IPLs). It also permutes
DNA and RNA states to create a background distribution to filter IPLs as a
way to remove events observed by chance. It provides multiple methods for
downstream analysis and visualization.
License: GPL-3
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Depends: R (>= 4.3)
Imports:
data.table (>= 1.14.2),
magrittr (>= 2.0.2),
BiocParallel (>= 1.28.3),
fitdistrplus (>= 1.1),
igraph (>= 1.2.11),
BiocSingular (>= 1.10.0),
S4Vectors (>= 0.32.3),
SingleCellExperiment (>= 1.16.0),
SummarizedExperiment (>= 1.24.0),
bluster (>= 1.4.0),
fgsea (>= 1.20.0),
scran (>= 1.22.1),
ComplexHeatmap (>= 2.16.0),
grid,
stats,
utils
Suggests:
rmarkdown,
knitr,
testthat (>= 3.0.0)
Config/testthat/edition: 3
VignetteBuilder: knitr
biocViews: Software, Technology, Sequencing, RNASeq, Survival, Clustering,
ImmunoOncology
SystemsRequirements: The `runPrd()` function requires an external software
named PARADIGM. For details, please see the 'Required external software'
section in vignette's 'Run PARADIGM: runPrd()'.
vjcitn
pliu55
lshep
Kayla-Morrell
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