RNAsense
Analysis of Time-Resolved RNA-Seq Data
Bioconductor version: 3.23 · Package version: 1.26.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RNAsense")Details
| Maintainer | Marcus Rosenblatt <marcus.rosenblatt@gmail.com> |
| Author | Marcus Rosenblatt [cre], Gao Meijang [aut], Helge Hass [aut], Daria Onichtchouk [aut] |
| License | GPL-3 |
| Bug Reports | https://github.com/marcusrosenblatt/RNAsense |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, RNASeq, Software |
| Package Short Url | https://bioconductor.org/packages/RNAsense/ |
Citation
From within R, enter citation("RNAsense"):
Gao Meijang, Helge Hass, Daria Onichtchouk. RNAsense: Analysis of Time-Resolved RNA-Seq Data. doi:10.18129/B9.bioc.RNAsense, R package version 1.26.0, https://bioconductor.org/packages/RNAsense.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | RNAsense_1.26.0.tar.gz |
| Windows binary (x86_64) | RNAsense_1.26.0.zip |
| macOS binary (arm64) | RNAsense_1.26.0.tgz |
| macOS binary (x86_64) | RNAsense_1.26.0.tgz |