icetea

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see icetea.

Integrating Cap Enrichment with Transcript Expression Analysis

Bioconductor version: 3.21

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 "4.5") and enter:


if (!require("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")

Analysing transcript 5'-profiling data using icetea HTML R Script

Reference Manual PDF

NEWS Text

LICENSE Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Transcriptomics

Version 1.26.0

In Bioconductor since BioC 3.8 (R-3.5) (7 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

System Requirements

URL https://github.com/vivekbhr/icetea

Bug Reports https://github.com/vivekbhr/icetea/issues

Suggests knitr, rmarkdown, Rsubread(>= 1.29.0), testthat

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 icetea_1.26.0.tar.gz

Windows Binary (x86_64) icetea_1.26.0.zip (64-bit only)

macOS Binary (x86_64) icetea_1.26.0.tgz

macOS Binary (arm64) icetea_1.26.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/icetea

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/icetea

Bioc Package Browser https://code.bioconductor.org/browse/icetea/

Package Short Url https://bioconductor.org/packages/icetea/

Package Downloads Report Download Stats