qrqc
Quick Read Quality Control
Bioconductor version: 2.10
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>
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("qrqc")
To cite this package in a publication, start R and enter:
citation("qrqc")
Documentation
| R Script | Using the qrqc package to gather information about sequence qualities | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DataImport, HighThroughputSequencing, Preprocessing, QualityControl, Sequencing, Software, Visualization |
| Depends | reshape, ggplot2, Biostrings, biovizBase, brew, xtable, Rsamtools(>= 1.3.28), testthat |
| Imports | reshape, ggplot2, Biostrings, biovizBase, graphics, methods, plyr, stats |
| Suggests | |
| System Requirements | |
| License | GPL (>=2) |
| URL | http://github.com/vsbuffalo/qrqc |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Version | 1.10.0 |
| Since | Bioconductor 2.8 (R-2.13) |
Package Downloads
| Package Source | qrqc_1.10.0.tar.gz |
| Windows Binary | qrqc_1.10.0.zip (32- & 64-bit) |
| MacOS 10.5 (Leopard) binary | qrqc_1.10.0.tgz |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Annotation
- Variants
- Flow Cytometry and other assays
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