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DESCRIPTION
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DESCRIPTION
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Package: OutSplice
Type: Package
Title: Comparison of Splicing Events between Tumor and Normal Samples
Version: 1.3.1
Authors@R: c(person("Joseph", "Bendik", role = "aut", comment = c(ORCID = "0000-0003-0877-5639")),
person("Sandhya", "Kalavacherla", role = "aut", comment = c(ORCID = "0000-0003-0485-9042")),
person("Michael", "Considine", role = "aut", comment = c(ORCID = "0000-0002-8666-4857")),
person("Bahman", "Afsari", role = "aut", comment = c(ORCID = "0000-0001-8717-7199")),
person("Michael F.", "Ochs", role = "aut"),
person("Joseph", "Califano", role = "aut", comment = c(ORCID = "0000-0002-4715-6761")),
person("Daria A.", "Gaykalova", role = "aut", comment = c(ORCID = "0000-0001-5037-0147")),
person("Elana", "Fertig", role = "aut", comment = c(ORCID = "0000-0003-3204-342X")),
person("Theresa", "Guo", email = "twguo@health.ucsd.edu", role = c("cre", "aut"), comment = c(ORCID = "0000-0002-1689-3275")))
Description: An easy to use tool that can compare splicing events in
tumor and normal tissue samples using either a user generated matrix, or
data from The Cancer Genome Atlas (TCGA). This package generates a matrix of
splicing outliers that are significantly over or underexpressed in tumors
samples compared to normal denoted by chromosome location. The package also
will calculate the splicing burden in each tumor and characterize the
types of splicing events that occur.
Encoding: UTF-8
License: GPL-2
Depends: R(>= 4.3)
Imports: AnnotationDbi (>= 1.60.0), GenomicRanges (>= 1.49.0),
GenomicFeatures (>= 1.50.2), IRanges (>= 2.32.0), org.Hs.eg.db (>= 3.16.0),
TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2),
TxDb.Hsapiens.UCSC.hg38.knownGene (>= 3.16.0), S4Vectors (>= 0.36.0)
Suggests: BiocStyle, knitr, rmarkdown, testthat
VignetteBuilder: knitr
biocViews: AlternativeSplicing, DifferentialExpression, DifferentialSplicing, GeneExpression, RNASeq, Software, VariantAnnotation
BugReports: https://github.com/GuoLabUCSD/OutSplice/issues
URL: https://github.com/GuoLabUCSD/OutSplice
RoxygenNote: 7.2.3