INSPEcT

This package is for version 3.6 of Bioconductor; for the stable, up-to-date release version, see INSPEcT.

Analysis of 4sU-seq and RNA-seq time-course data


Bioconductor version: 3.6

INSPEcT (INference of Synthesis, Processing and dEgradation rates in Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and asses via modeling the rates that determines changes in mature mRNA levels.

Author: Stefano de Pretis

Maintainer: Stefano de Pretis <ste.depo at gmail.com>

Citation (from within R, enter citation("INSPEcT")):

Installation

To install this package, start R (version "3.4") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("INSPEcT")

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("INSPEcT")
INSPEcT PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneRegulation, RNASeq, Sequencing, Software, SystemsBiology, TimeCourse
Version 1.8.0
In Bioconductor since BioC 3.2 (R-3.2) (8.5 years)
License GPL-2
Depends R (>= 3.2), methods, Biobase, BiocParallel
Imports pROC, deSolve, rootSolve, compiler, preprocessCore, GenomicFeatures, GenomicRanges, IRanges, BiocGenerics, GenomicAlignments, Rsamtools, S4Vectors
System Requirements
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Suggests BiocStyle, knitr, TxDb.Mmusculus.UCSC.mm9.knownGene
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package INSPEcT_1.8.0.tar.gz
Windows Binary INSPEcT_1.8.0.zip
Mac OS X 10.11 (El Capitan) INSPEcT_1.8.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/INSPEcT
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/INSPEcT
Package Short Url https://bioconductor.org/packages/INSPEcT/
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Old Source Packages for BioC 3.6 Source Archive