DOI: 10.18129/B9.bioc.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 (3.17)

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")):


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HTML R Script Analysing transcript 5'-profiling data using icetea
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biocViews DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Transcriptomics
Version 1.17.0
In Bioconductor since BioC 3.8 (R-3.5) (4 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
Suggests knitr, rmarkdown, Rsubread(>= 1.29.0), testthat
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