This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see QuasR.
Bioconductor version: 3.10
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 (from within R,
enter citation("QuasR")
):
To install this package, start R (version "3.6") and enter:
if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("QuasR")
For older versions of R, please refer to the appropriate Bioconductor release.
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("QuasR")
HTML | R Script | An introduction to QuasR |
Reference Manual | ||
Text | NEWS |
biocViews | Alignment, ChIPSeq, Coverage, Genetics, ImmunoOncology, MethylSeq, Preprocessing, QualityControl, RNASeq, Sequencing, Software |
Version | 1.26.0 |
In Bioconductor since | BioC 2.12 (R-3.0) (7 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 |
LinkingTo | Rhtslib(>= 1.15.3) |
Suggests | Gviz, BiocStyle, knitr, rmarkdown, covr, testthat |
SystemRequirements | GNU make |
Enhances | |
URL | |
Depends On Me | |
Imports Me | |
Suggests Me | |
Links To Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | QuasR_1.26.0.tar.gz |
Windows Binary | QuasR_1.26.0.zip |
Mac OS X 10.11 (El Capitan) | QuasR_1.26.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/QuasR |
Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/QuasR |
Package Short Url | https://bioconductor.org/packages/QuasR/ |
Package Downloads Report | Download Stats |
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