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DESCRIPTION
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DESCRIPTION
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Type: Package
Package: decoupleR
Title: decoupleR: Ensemble of computational methods to infer biological activities from omics data
Version: 2.9.7
Authors@R:
c(person(given = "Pau",
family = "Badia-i-Mompel",
role = c("aut","cre"),
email = "pau.badia@uni-heidelberg.de",
comment = c(ORCID = "0000-0002-1004-3923")),
person(given = "Jesús",
family = "Vélez-Santiago",
role = c("aut"),
email = "jvelezmagic@gmail.com",
comment = c(ORCID = "0000-0001-5128-3838")),
person(given = "Jana",
family = "Braunger",
role = c("aut"),
email = "jana.bc@gmx.de",
comment = c(ORCID = "0000-0003-0820-9987")),
person(given = "Celina",
family = "Geiss",
role = c("aut"),
email = "celina.geiss@stud.uni-heidelberg.de",
comment = c(ORCID = "0000-0002-8740-706X")),
person(given = "Daniel",
family = "Dimitrov",
role = c("aut"),
email = "daniel.dimitrov@uni-heidelberg.de",
comment = c(ORCID = "0000-0002-5197-2112")),
person(given = "Sophia",
family = "Müller-Dott",
role = c("aut"),
email = "sophia.mueller-dott@uni-heidelberg.de",
comment = c(ORCID = "0000-0002-9710-1865")),
person(given = "Petr",
family = "Taus",
role = c("aut"),
email = "petr.taus@ceitec.muni.cz",
comment = c(ORCID = "0000-0003-3764-9033")),
person(given = "Aurélien",
family = "Dugourd",
role = c("aut"),
email = "aurelien.dugourd@bioquant.uni-heidelberg.de",
comment = c(ORCID = "0000-0002-0714-028X")),
person(given = "Christian H.",
family = "Holland",
role = "aut",
email = "cholland2408@gmail.com",
comment = c(ORCID = "0000-0002-3060-5786")),
person(given = "Ricardo O.",
family = "Ramirez Flores",
role = c("aut"),
email = "roramirezf@uni-heidelberg.de ",
comment = c(ORCID = "0000-0003-0087-371X")),
person(given = "Julio",
family = "Saez-Rodriguez",
role = c("aut"),
email = "pub.saez@uni-heidelberg.de",
comment = c(ORCID = "0000-0002-8552-8976"))
)
Description: Many methods allow us to extract biological activities from omics
data using information from prior knowledge resources, reducing the
dimensionality for increased statistical power and better interpretability.
Here, we present decoupleR, a Bioconductor package containing different
statistical methods to extract these signatures within a unified framework.
decoupleR allows the user to flexibly test any method with any resource.
It incorporates methods that take into account the sign and weight of
network interactions. decoupleR can be used with any omic, as long as its
features can be linked to a biological process based on prior knowledge.
For example, in transcriptomics gene sets regulated by a transcription
factor, or in phospho-proteomics phosphosites that are targeted by a kinase.
License: GPL-3 + file LICENSE
URL: https://saezlab.github.io/decoupleR/
BugReports: https://github.com/saezlab/decoupleR/issues
Depends:
R (>= 4.0)
Imports:
BiocParallel,
broom,
dplyr,
magrittr,
Matrix,
parallelly,
purrr,
rlang,
stats,
stringr,
tibble,
tidyr,
tidyselect,
withr
Suggests:
glmnet (>= 4.1-7),
GSVA,
viper,
fgsea (>= 1.15.4),
AUCell,
SummarizedExperiment,
rpart,
ranger,
BiocStyle,
covr,
knitr,
pkgdown,
RefManageR,
rmarkdown,
roxygen2,
sessioninfo,
pheatmap,
testthat,
OmnipathR,
Seurat,
ggplot2,
ggrepel,
patchwork,
magick
VignetteBuilder:
knitr
biocViews: DifferentialExpression, FunctionalGenomics, GeneExpression,
GeneRegulation, Network, Software, StatisticalMethod, Transcription,
Config/testthat/edition: 3
Encoding: UTF-8
LazyData: false
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.0