icetea
Integrating Cap Enrichment with Transcript Expression Analysis
Bioconductor version: Release (3.20)
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("icetea")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, ImmunoOncology, RNASeq, Sequencing, Software, Transcription, Transcriptomics |
| Version | 1.24.0 |
| In Bioconductor since | BioC 3.8 (R-3.5) (6 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 |
| 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_1.24.0.tar.gz |
| Windows Binary (x86_64) | icetea_1.24.0.zip (64-bit only) |
| macOS Binary (x86_64) | icetea_1.24.0.tgz |
| macOS Binary (arm64) | icetea_1.24.0.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 |