DESCRIPTION

Package: RNAsense
Type: Package
Title: Analysis of Time-Resolved RNA-Seq Data
Version: 0.99.27
Authors@R: c(person("Marcus", "Rosenblatt", email = "marcus.rosenblatt@gmail.com", role = c("aut", "cre")),
    person("Gao", "Meijang", role = "aut"),
    person("Helge", "Hass", role = "aut"),
    person("Jens", "Timmer", 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 (>= 3.5)
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