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INSPEcT

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

Modeling RNA synthesis, processing and degradation with RNA-seq data

Bioconductor version: Development (3.18)

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

Author: Stefano de Pretis

Maintainer: Stefano de Pretis <ste.depo at gmail.com>, Mattia Furlan <Mattia.Furlan at iit.it>

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

Installation

To install this package, start R (version "4.3") and enter: 

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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 - INference of Synthesis, Processing and dEgradation rates from Transcriptomic data HTML R Script
INSPEcT_GUI.html HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews GeneRegulation, RNASeq, Sequencing, Software, SystemsBiology, TimeCourse
Version 1.31.0
In Bioconductor since BioC 3.2 (R-3.2) (8 years)
License GPL-2
Depends R (>= 3.6), methods, Biobase, BiocParallel
Imports pROC, deSolve, rootSolve, KernSmooth, gdata, GenomicFeatures, GenomicRanges, IRanges, BiocGenerics, GenomicAlignments, Rsamtools, S4Vectors, GenomeInfoDb, DESeq2, plgem, rtracklayer, SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny
Linking To
Suggests BiocStyle, knitr, rmarkdown
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Package Archives

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

Source Package INSPEcT_1.31.0.tar.gz
Windows Binary INSPEcT_1.31.0.zip (64-bit only)
macOS Binary (x86_64) INSPEcT_1.31.0.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/INSPEcT
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/INSPEcT
Bioc Package Browser https://code.bioconductor.org/browse/INSPEcT/
Package Short Url https://bioconductor.org/packages/INSPEcT/
Package Downloads Report Download Stats