INSPEcT

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see INSPEcT.

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

Bioconductor version: 3.13

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 "4.1") 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 - INference of Synthesis, Processing and dEgradation rates from Transcriptomic data HTML R Script

INSPEcT_GUI.html HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews GeneRegulation, RNASeq, Sequencing, Software, SystemsBiology, TimeCourse

Version 1.22.0

In Bioconductor since BioC 3.2 (R-3.2) (8.5 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

System Requirements

URL

Suggests BiocStyle, knitr, rmarkdown

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Build Report Build Report

Package Archives

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

Source Package INSPEcT_1.22.0.tar.gz

Windows Binary INSPEcT_1.22.0.zip

macOS 10.13 (High Sierra) INSPEcT_1.22.0.tgz

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

Old Source Packages for BioC 3.13 Source Archive