To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("qrqc")
In most cases, you don't need to download the package archive at all.
qrqc
Quick Read Quality Control
Bioconductor version: 2.14
Quickly scans reads and gathers statistics on base and quality frequencies, read length, k-mers by position, and frequent sequences. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report. S4 SequenceSummary objects allow specific tests and functionality to be written around the data collected.
Author: Vince Buffalo
Maintainer: Vince Buffalo <vsbuffalo at ucdavis.edu>
Citation (from within R,
enter citation("qrqc")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("qrqc")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("qrqc")
| R Script | Using the qrqc package to gather information about sequence qualities | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, Preprocessing, QualityControl, Sequencing, Software, Visualization |
| Version | 1.18.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) |
| License | GPL (>=2) |
| Depends | reshape, ggplot2, Biostrings, biovizBase, brew, xtable, Rsamtools(>= 1.3.28), testthat |
| Imports | reshape, ggplot2, Biostrings, biovizBase, graphics, methods, plyr, stats |
| Suggests | |
| System Requirements | |
| URL | http://github.com/vsbuffalo/qrqc |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | qrqc_1.18.0.tar.gz |
| Windows Binary | qrqc_1.18.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | qrqc_1.18.0.tgz |
| Mac OS X 10.9 (Mavericks) | qrqc_1.18.0.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
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