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HTSeqGenie

A NGS analysis pipeline.


Bioconductor version: Release (3.18)

Libraries to perform NGS analysis.

Author: Gregoire Pau, Jens Reeder

Maintainer: Jens Reeder <reeder.jens at gene.com>

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

Installation

To install this package, start R (version "4.3") and enter:


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("HTSeqGenie")

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("HTSeqGenie")
HTSeqGenie PDF R Script
Reference Manual PDF
NEWS Text

Details

biocViews Software
Version 4.32.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License Artistic-2.0
Depends R (>= 3.5.0), gmapR(>= 1.8.0), ShortRead(>= 1.19.13), VariantAnnotation(>= 1.8.3)
Imports BiocGenerics(>= 0.2.0), S4Vectors(>= 0.9.25), IRanges(>= 1.21.39), GenomicRanges(>= 1.23.21), Rsamtools(>= 1.8.5), Biostrings(>= 2.24.1), chipseq(>= 1.6.1), hwriter (>= 1.3.0), Cairo (>= 1.5.5), GenomicFeatures(>= 1.9.31), BiocParallel, parallel, tools, rtracklayer(>= 1.17.19), GenomicAlignments, VariantTools(>= 1.7.7), GenomeInfoDb, SummarizedExperiment, methods
System Requirements
URL
See More
Suggests TxDb.Hsapiens.UCSC.hg19.knownGene, LungCancerLines, org.Hs.eg.db, RUnit
Linking To
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Package Archives

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

Source Package HTSeqGenie_4.32.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/HTSeqGenie
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/HTSeqGenie
Bioc Package Browser https://code.bioconductor.org/browse/HTSeqGenie/
Package Short Url https://bioconductor.org/packages/HTSeqGenie/
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