HTSeqGenie
This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.21 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see HTSeqGenie.
A NGS analysis pipeline.
Bioconductor version: Release (3.21)
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 "4.5") 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
| Reference Manual |
Details
| biocViews | Software |
| Version | 4.38.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (13 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), pwalign, 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 | |
| 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 | |
| Windows Binary (x86_64) | |
| 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 |
| Package Short Url | https://bioconductor.org/packages/HTSeqGenie/ |
| Package Downloads Report | Download Stats |