QuasR
Quantify and Annotate Short Reads in R
Bioconductor version: Release (3.19)
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. Read alignments are either generated through Rbowtie (data from DNA/ChIP/ATAC/Bis-seq experiments) or Rhisat2 (data from RNA-seq experiments that require spliced alignments), or can be provided in the form of bam files.
Author: Anita Lerch [aut], Adam Alexander Thil SMITH [aut] 
, Charlotte Soneson [aut] , Dimos Gaidatzis [aut], Michael Stadler [aut, cre]
Maintainer: Michael Stadler <michael.stadler at fmi.ch>
citation("QuasR")):
Installation
To install this package, start R (version "4.4") 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 | 1.44.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11.5 years) |
| License | GPL-2 |
| Depends | R (>= 4.4), parallel, GenomicRanges, Rbowtie |
| Imports | methods, grDevices, graphics, utils, stats, tools, BiocGenerics, S4Vectors, IRanges, Biobase, Biostrings, BSgenome, Rsamtools(>= 2.13.1), GenomicFeatures, txdbmaker, ShortRead, BiocParallel, GenomeInfoDb, rtracklayer, GenomicFiles, AnnotationDbi |
| System Requirements | GNU make |
| URL | https://bioconductor.org/packages/QuasR |
| Bug Reports | https://github.com/fmicompbio/QuasR/issues |
See More
| Suggests | Gviz, BiocStyle, GenomicAlignments, Rhisat2, knitr, rmarkdown, covr, testthat |
| Linking To | Rhtslib(>= 1.99.1) |
| Enhances | |
| Depends On Me | |
| Imports Me | SingleMoleculeFootprinting |
| Suggests Me | eisaR |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | QuasR_1.44.0.tar.gz |
| Windows Binary (x86_64) | QuasR_1.44.0.zip (64-bit only) |
| macOS Binary (x86_64) | QuasR_1.44.0.tgz |
| macOS Binary (arm64) | QuasR_1.44.0.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 |