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Bioconductor - icetea (development version)

icetea

This is the development version of icetea; for the stable release version, see icetea.

Integrating Cap Enrichment with Transcript Expression Analysis

Bioconductor version: Development (3.22)

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")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Details biocViews DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Transcriptomics Version 1.27.0 In Bioconductor since BioC 3.8 (R-3.5) (6.5 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 Package Archives

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

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