icetea

DOI: 10.18129/B9.bioc.icetea    

This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see icetea.

Integrating Cap Enrichment with Transcript Expression Analysis

Bioconductor version: 3.12

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 <v.bhardwaj at hubrecht.eu>

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

Installation

To install this package, start R (version "4.0") 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 1.8.0
In Bioconductor since BioC 3.8 (R-3.5) (2.5 years)
License GPL-3 + file LICENSE
Depends R (>= 4.0)
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_1.8.0.tar.gz
Windows Binary icetea_1.8.0.zip
macOS 10.13 (High Sierra) icetea_1.8.0.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 https://bioconductor.org/packages/icetea/
Package Downloads Report Download Stats

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