QuasR
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see QuasR.
Quantify and Annotate Short Reads in R
Bioconductor version: 3.9
This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.
Author: Anita Lerch, Charlotte Soneson, Dimos Gaiditzis and Michael Stadler
Maintainer: Michael Stadler <michael.stadler at fmi.ch>
citation("QuasR")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("QuasR")
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("QuasR")| An introduction to QuasR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, ChIPSeq, Coverage, Genetics, ImmunoOncology, MethylSeq, Preprocessing, QualityControl, RNASeq, Sequencing, Software |
| Version | 1.24.2 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11 years) |
| License | GPL-2 |
| Depends | R (>= 3.6), parallel, GenomicRanges(>= 1.13.3), Rbowtie |
| Imports | methods, grDevices, graphics, utils, BiocGenerics, S4Vectors(>= 0.9.25), IRanges, BiocManager, Biobase, Biostrings, BSgenome, Rsamtools(>= 1.99.1), GenomicFeatures(>= 1.17.13), ShortRead(>= 1.19.1), GenomicAlignments, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, Rhisat2, AnnotationDbi |
| System Requirements | |
| URL |
See More
| Suggests | Gviz, BiocStyle, knitr, rmarkdown, covr, testthat |
| Linking To | Rhtslib(>= 1.15.3) |
| 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 | QuasR_1.24.2.tar.gz |
| Windows Binary | QuasR_1.24.2.zip |
| Mac OS X 10.11 (El Capitan) | QuasR_1.24.2.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/QuasR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/QuasR |
| Bioc Package Browser | https://code.bioconductor.org/browse/QuasR/ |
| Package Short Url | https://bioconductor.org/packages/QuasR/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |