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 (3.24)
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("INSPEcT")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | ||
| NEWS | Text |
Details
| biocViews | GeneRegulation, RNASeq, Sequencing, Software, SystemsBiology, TimeCourse |
| Version | 1.43.0 |
| In Bioconductor since | BioC 3.2 (R-3.2) (11 years) |
| License | GPL-2 |
| Depends | R (>= 3.6), methods, Biobase, BiocParallel |
| Imports | pROC, deSolve, rootSolve, KernSmooth, readxl, GenomicFeatures, GenomicRanges, IRanges, BiocGenerics, GenomicAlignments, Rsamtools, S4Vectors, Seqinfo, DESeq2, plgem, rtracklayer, SummarizedExperiment, TxDb.Mmusculus.UCSC.mm9.knownGene, shiny |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, 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 | INSPEcT_1.43.0.tar.gz |
| Windows Binary (x86_64) | INSPEcT_1.43.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | INSPEcT_1.43.0.tgz |
| macOS Binary (sonoma-arm64) | INSPEcT_1.43.0.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 |