icetea

DOI: 10.18129/B9.bioc.icetea    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see icetea.

Integrating Cap Enrichment with Transcript Expression Analysis

Bioconductor version: 3.9

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>

Installation

To install this package, start R (version "3.6") and enter:

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

BiocManager::install("icetea")

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, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version	1.2.0
In Bioconductor since	BioC 3.8 (R-3.5) (1 year)
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, DESeq2, 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_1.2.0.tar.gz
Windows Binary	icetea_1.2.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	icetea_1.2.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/icetea
Source Repository (Developer Access)	git clone [email protected]:packages/icetea
Package Short Url	https://bioconductor.org/packages/icetea/
Package Downloads Report	Download Stats