To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("TEQC")
In most cases, you don't need to download the package archive at all.
TEQC
Quality control for target capture experiments
Bioconductor version: 2.14
Target capture experiments combine hybridization-based (in solution or on microarrays) capture and enrichment of genomic regions of interest (e.g. the exome) with high throughput sequencing of the captured DNA fragments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.
Author: M. Hummel, S. Bonnin, E. Lowy, G. Roma
Maintainer: Manuela Hummel <m.hummel at dkfz.de>
Citation (from within R,
enter citation("TEQC")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("TEQC")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("TEQC")
| R Script | TEQC | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | Genetics, Microarray, QualityControl, Sequencing, Software |
| Version | 3.4.0 |
| In Bioconductor since | BioC 2.8 (R-2.13) |
| License | GPL (>= 2) |
| Depends | methods, BiocGenerics(>= 0.1.0), IRanges(>= 1.13.5), Rsamtools, hwriter |
| Imports | Biobase(>= 2.15.1) |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | TEQC_3.4.0.tar.gz |
| Windows Binary | TEQC_3.4.0.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | TEQC_3.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | TEQC_3.4.0.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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