Registration Open for Bioc2024 July 24-26


Integrating Cap Enrichment with Transcript Expression Analysis

Bioconductor version: Release (3.19)

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>

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


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

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


biocViews DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.22.0
In Bioconductor since BioC 3.8 (R-3.5) (5.5 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
System Requirements
Bug Reports
See More
Suggests knitr, rmarkdown, Rsubread(>= 1.29.0), testthat
Linking To
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_1.22.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) icetea_1.22.0.tgz
macOS Binary (arm64) icetea_1.22.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
Bioc Package Browser
Package Short Url
Package Downloads Report Download Stats