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icetea

Integrating Cap Enrichment with Transcript Expression Analysis


Bioconductor version: Release (3.18)

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 "4.3") 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

Details

biocViews DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.20.0
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
URL https://github.com/vivekbhr/icetea
Bug Reports https://github.com/vivekbhr/icetea/issues
See More
Suggests knitr, rmarkdown, Rsubread(>= 1.29.0), testthat
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package icetea_1.20.0.tar.gz
Windows Binary icetea_1.20.0.zip
macOS Binary (x86_64) icetea_1.20.0.tgz
macOS Binary (arm64) icetea_1.20.0.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