Package: RNAsense
Type: Package
Title: Analysis of Time-Resolved RNA-Seq Data
Version: 1.24.0
Authors@R: c(person("Marcus", "Rosenblatt", email = "marcus.rosenblatt@gmail.com", role = "cre"),
    person("Gao", "Meijang", role = "aut"),
    person("Helge", "Hass", role = "aut"),
    person("Daria", "Onichtchouk", role = "aut"))
Description: RNA-sense tool compares RNA-seq time curves in two
        experimental conditions, i.e. wild-type and mutant, and works
        in three steps. At Step 1, it builds expression profile for
        each transcript in one condition (i.e. wild-type) and tests if
        the transcript abundance grows or decays significantly.
        Dynamic transcripts are then sorted to non-overlapping groups
        (time profiles) by the time point of switch up or down. At Step
        2, RNA-sense outputs the groups of differentially expressed
        transcripts, which are up- or downregulated in the mutant
        compared to the wild-type at each time point. At Step 3,
        Correlations (Fisher's exact test) between the outputs of Step
        1 (switch up- and switch down- time profile groups) and the
        outputs of Step2 (differentially expressed transcript groups)
        are calculated. The results of the correlation analysis are
        printed as two-dimensional color plot, with time profiles and
        differential expression groups at y- and x-axis, respectively,
        and facilitates the biological interpretation of the data.
License: GPL-3
Encoding: UTF-8
LazyData: false
Depends: R (>= 3.6)
RoxygenNote: 6.1.1
BugReports: https://github.com/marcusrosenblatt/RNAsense
biocViews: RNASeq, GeneExpression, DifferentialExpression
Imports: ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment,
        stats, utils, methods
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Config/pak/sysreqs: libicu-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:55:39 UTC
RemoteUrl: https://github.com/bioc/RNAsense
RemoteRef: RELEASE_3_22
RemoteSha: 7827d43a47674e0ff613e3168a43eba8ad19d25a
NeedsCompilation: no
Packaged: 2025-11-11 17:05:21 UTC; root
Author: Marcus Rosenblatt [cre],
  Gao Meijang [aut],
  Helge Hass [aut],
  Daria Onichtchouk [aut]
Maintainer: Marcus Rosenblatt <marcus.rosenblatt@gmail.com>
Built: R 4.5.2; ; 2025-11-11 17:12:06 UTC; windows
