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DESCRIPTION
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DESCRIPTION
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Package: TBSignatureProfiler
Title: Profile RNA-Seq Data Using TB Pathway Signatures
Version: 1.17.1
Authors@R: c(
person("Aubrey R.", "Odom", , "[email protected]", role = c("aut", "cre", "dtm"),
comment = c(ORCID = "0000-0001-7113-7598")),
person("David", "Jenkins", , "[email protected]", role = c("aut", "org"),
comment = c(ORCID = "0000-0002-7451-4288")),
person("Xutao", "Wang", , "[email protected]", role = "aut"),
person("Yue", "Zhao", , "[email protected]", role = "ctb",
comment = c(ORCID = "0000-0001-5257-5103")),
person("Christian", "Love", , "[email protected]", role = "ctb"),
person("W. Evan", "Johnson", , "[email protected]", role = "aut")
)
Description: Gene signatures of TB progression, TB disease, and other TB
disease states have been validated and published previously. This
package aggregates known signatures and provides computational tools
to enlist their usage on other datasets. The TBSignatureProfiler makes
it easy to profile RNA-Seq data using these signatures and includes
common signature profiling tools including ASSIGN, GSVA, and ssGSEA.
Original models for some gene signatures are also available. A shiny
app provides some functionality alongside for detailed command line
accessibility.
License: MIT + file LICENSE
URL: https://github.com/wejlab/TBSignatureProfiler
https://wejlab.github.io/TBSignatureProfiler-docs/
BugReports: https://github.com/wejlab/TBSignatureProfiler/issues
Depends:
R (>= 4.2.0)
Imports:
ASSIGN (>= 1.23.1),
BiocParallel,
ComplexHeatmap,
DESeq2,
DT,
edgeR,
gdata,
ggplot2,
GSVA (>= 1.51.3),
magrittr,
methods,
RColorBrewer,
reshape2,
rlang,
ROCit,
S4Vectors,
singscore,
stats,
SummarizedExperiment
Suggests:
BiocStyle,
caret,
circlize,
class,
covr,
dplyr,
e1071,
glmnet,
HGNChelper,
impute,
knitr,
lintr,
MASS,
plyr,
pROC,
randomForest,
rmarkdown,
shiny,
spelling,
sva,
testthat
VignetteBuilder:
knitr
biocViews: GeneExpression, DifferentialExpression
Encoding: UTF-8
Language: en-US
LazyData: TRUE
RoxygenNote: 7.3.1
Roxygen: list(markdown = TRUE)