INSPEcT

DOI: 10.18129/B9.bioc.INSPEcT    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see INSPEcT.

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

Bioconductor version: 3.8

INSPEcT (INference of Synthesis, Processing and dEgradation rates from Transcriptomic data) RNA-seq data in time-course experiments or different conditions, with or without the support of nascent RNA data.

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 "3.5") and enter:

if (!requireNamespace("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")

 

PDF R Script INSPEcT
PDF R Script RNAdynamics
PDF   Reference Manual
Text   NEWS

Details

biocViews GeneRegulation, RNASeq, Sequencing, Software, SystemsBiology, TimeCourse
Version 1.12.2
In Bioconductor since BioC 3.2 (R-3.2) (3.5 years)
License GPL-2
Depends R (>= 3.2), methods, Biobase, BiocParallel
Imports pROC, deSolve, rootSolve, compiler, preprocessCore, GenomicFeatures, GenomicRanges, IRanges, BiocGenerics, GenomicAlignments, Rsamtools, S4Vectors, DESeq2, plgem, SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny
LinkingTo
Suggests BiocStyle, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package INSPEcT_1.12.2.tar.gz
Windows Binary INSPEcT_1.12.2.zip
Mac OS X 10.11 (El Capitan) INSPEcT_1.12.2.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 http://bioconductor.org/packages/INSPEcT/
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