QDNAseq: Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Data Types https://www.bioconductor.org/packages/aroma.light/
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Nitesh Turaga d0d6442358 bump x.y.z version to odd y after creation of RELEASE_3_10 branch 5 months ago
R BUG FIX: plot() positioned segments that were out of range incorrectly [PR#61,#73] 6 months ago
data Adds alsace/ Basic4Cseq/ CAFE/ COPDSexualDimorphism/ INPower/ massiR/ metaseqR/ MLSeq/ pxr/ QDNAseq/ Rcpi/ sapFinder/ UNDO/ viper/ to the repos. 6 years ago
inst README: Rewrite and restructure 6 months ago
man Utilize QDNAseq.{hg19,mm10} packages instead of download bin annotations from the cloud [#67] 7 months ago
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tests Travis CI: trying to get the cache built 6 months ago
vignettes Link to the 'GEM library' tool was broken [#80] 6 months ago
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Makefile Commit made by the Bioconductor Git-SVN bridge. 5 years ago
NAMESPACE Utilize QDNAseq.{hg19,mm10} packages instead of download bin annotations from the cloud [#67] 7 months ago
NEWS QDNAseq 1.21.6 6 months ago
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README.md

QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations

This repository contains source code for the R/Bioconductor package QDNAseq, which implements the QDNAseq method (Scheinin et al., 2014). For instructions on how to use QDNAseq, see the ‘Introduction to QDNAseq’ vignette, which also installed together with the package. Please remember to cite Scheinin et al. (2014) whenever using QDNAseq in your research.

Please use the official Bioconductor instructions for installation QDNAseq;

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("QDNAseq")

To analyze human data, the QDNAseq.hg19 package must be installed;

BiocManager::install("QDNAseq.hg19")

To analyze mouse data, the QDNAseq.mm10 package must be installed;

BiocManager::install("QDNAseq.mm10")

To install the devel versions of QDNAseq, QDNAseq.hg19, and QDNAseq.mm10, see the Bioconductor devel installation instruction.

References

  • Scheinin I, Sie D, Bengtsson H, van de Wiel MA, Olshen AB, van Thuijl HF, van Essen HF, Eijk PP, Rustenburg F, Meijer GA, Reijneveld JC, Wesseling P, Pinkel D, Albertson DG and Ylstra B. DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Research 24: 2022-2032, 2014. PMC4248318

Software quality

  • R CMD check status on Bioconductor: BUILD/CHECK Report (devel), BUILD/CHECK Report (release)
  • R CMD check --as-cran status on Travis CI: Build Status
  • Test code coverage: Coverage Status

GitHub repository and Bioconductor repository

This GitHub repository is (manually) kept in sync with the Bioconductor devel version of the QDNAseq package. More precisely, the master branch in this GitHub repository is in sync with what is on the Bioconductor git repository (e.g. git clone https://git.bioconductor.org/packages/QDNAseq). The source code previous versions is available via git tags, e.g. QDNAseq 1.21.1.