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DESCRIPTION
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DESCRIPTION
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Package: proActiv
Title: Estimate Promoter Activity from RNA-Seq data
Version: 1.3.4
Authors@R: c(
person(given = "Deniz",
family = "Demircioglu",
role = c("aut"),
email = "[email protected]",
comment = c(ORCID = "0000-0001-7857-0407")),
person(given = "Jonathan",
family = "Göke",
role = c("aut"),
email = "[email protected]"),
person(given = "Joseph",
family = "Lee",
role = c("cre"),
email = "[email protected]"))
Description: Most human genes have multiple promoters that control the
expression of different isoforms. The use of these alternative promoters
enables the regulation of isoform expression pre-transcriptionally.
Alternative promoters have been found to be important in a wide number of cell
types and diseases. proActiv is an R package that enables the analysis of
promoters from RNA-seq data. proActiv uses aligned reads as input, and
generates counts and normalized promoter activity estimates for each annotated
promoter. In particular, proActiv accepts junction files from TopHat2 or STAR
or BAM files as inputs. These estimates can then be used to identify which
promoter is active, which promoter is inactive, and which promoters change
their activity across conditions. proActiv also allows visualization of
promoter activity across conditions.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 4.0.0)
RoxygenNote: 7.1.1
Imports:
AnnotationDbi,
BiocParallel,
data.table,
dplyr,
DESeq2,
IRanges,
GenomicRanges,
GenomicFeatures,
GenomicAlignments,
GenomeInfoDb,
ggplot2,
gplots,
graphics,
methods,
rlang,
scales,
S4Vectors,
SummarizedExperiment,
stats,
tibble
Suggests:
testthat,
rmarkdown,
knitr,
Rtsne,
gridExtra
URL: https://github.com/GoekeLab/proActiv
biocViews:
RNASeq,
GeneExpression,
Transcription,
AlternativeSplicing,
GeneRegulation,
DifferentialSplicing,
FunctionalGenomics,
Epigenetics,
Transcriptomics,
Preprocessing
VignetteBuilder: knitr