HTSeqGenie

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see HTSeqGenie.

A NGS analysis pipeline.


Bioconductor version: 3.9

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 "3.6") 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 4.14.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 years)
License Artistic-2.0
Depends R (>= 3.0.0), 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
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 HTSeqGenie_4.14.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
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/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive