RNAsense
Analysis of Time-Resolved RNA-Seq Data
Bioconductor version: Release (3.20)
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>
citation("RNAsense")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("RNAsense")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("RNAsense")| Put the title of your vignette here | HTML | R Script |
| Reference Manual |
Details
| biocViews | DifferentialExpression, GeneExpression, RNASeq, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (5 years) |
| License | GPL-3 |
| Depends | R (>= 3.6) |
| Imports | ggplot2, parallel, NBPSeq, qvalue, SummarizedExperiment, stats, utils, methods |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/marcusrosenblatt/RNAsense |
See More
| Suggests | knitr, rmarkdown |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | RNAsense_1.20.0.tar.gz |
| Windows Binary (x86_64) | RNAsense_1.20.0.zip (64-bit only) |
| macOS Binary (x86_64) | RNAsense_1.20.0.tgz |
| macOS Binary (arm64) | RNAsense_1.19.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/RNAsense |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/RNAsense |
| Bioc Package Browser | https://code.bioconductor.org/browse/RNAsense/ |
| Package Short Url | https://bioconductor.org/packages/RNAsense/ |
| Package Downloads Report | Download Stats |