icetea

DOI: 10.18129/B9.bioc.icetea    

Integrating Cap Enrichment with Transcript Expression Analysis

Bioconductor version: Release (3.8)

icetea (Integrating Cap Enrichment with Transcript Expression Analysis) provides functions for end-to-end analysis of multiple 5'-profiling methods such as CAGE, RAMPAGE and MAPCap, beginning from raw reads to detection of transcription start sites using replicates. It also allows performing differential TSS detection between group of samples, therefore, integrating the mRNA cap enrichment information with transcript expression analysis.

Author: Vivek Bhardwaj [aut, cre]

Maintainer: Vivek Bhardwaj <bhardwaj at ie-freiburg.mpg.de>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("icetea", version = "3.8")

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("icetea")

 

HTML R Script Analysing transcript 5'-profiling data using icetea
PDF   Reference Manual
Text   NEWS
Text   LICENSE

Details

biocViews DifferentialExpression, GeneExpression, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.0.0
License GPL-3 + file LICENSE
Depends R (>= 3.5)
Imports stats, utils, methods, graphics, grDevices, ggplot2, GenomicFeatures, ShortRead, BiocParallel, Biostrings, S4Vectors, Rsamtools, BiocGenerics, IRanges, GenomicAlignments, GenomicRanges, rtracklayer, SummarizedExperiment, VariantAnnotation, limma, edgeR, csaw, TxDb.Dmelanogaster.UCSC.dm6.ensGene
LinkingTo
Suggests knitr, rmarkdown, Rsubread(>= 1.29.0), testthat
SystemRequirements
Enhances
URL https://github.com/vivekbhr/icetea
BugReports https://github.com/vivekbhr/icetea/issues
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 icetea_1.0.0.tar.gz
Windows Binary icetea_1.0.0.zip
Mac OS X 10.11 (El Capitan) icetea_1.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/icetea
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/icetea
Package Short Url http://bioconductor.org/packages/icetea/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: