DOI: 10.18129/B9.bioc.RNAsense    

This is the development version of RNAsense; for the stable release version, see RNAsense.

Analysis of Time-Resolved RNA-Seq Data

Bioconductor version: Development (3.15)

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.

Author: Marcus Rosenblatt [cre], Gao Meijang [aut], Helge Hass [aut], Daria Onichtchouk [aut]

Maintainer: Marcus Rosenblatt <marcus.rosenblatt at gmail.com>

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biocViews DifferentialExpression, GeneExpression, RNASeq, Software
Version 1.9.1
In Bioconductor since BioC 3.10 (R-3.6) (2 years)
License GPL-3
Depends R (>= 3.6)
Imports ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment, stats, utils, methods
Suggests knitr, rmarkdown
BugReports https://github.com/marcusrosenblatt/RNAsense
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Source Package RNAsense_1.9.1.tar.gz
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