Package: OmicsQC 1.1.0

OmicsQC: Nominating Quality Control Outliers in Genomic Profiling Studies

A method that analyzes quality control metrics from multi-sample genomic sequencing studies and nominates poor quality samples for exclusion. Per sample quality control data are transformed into z-scores and aggregated. The distribution of aggregated z-scores are modelled using parametric distributions. The parameters of the optimal model, selected either by goodness-of-fit statistics or user-designation, are used for outlier nomination. Two implementations of the Cosine Similarity Outlier Detection algorithm are provided with flexible parameters for dataset customization.

Authors:Anders Hugo Frelin [aut], Helen Zhu [aut], Paul C. Boutros [aut, cre]

OmicsQC_1.1.0.tar.gz
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OmicsQC.pdf |OmicsQC.html
OmicsQC/json (API)
NEWS

# Install 'OmicsQC' in R:
install.packages('OmicsQC', repos = c('https://pboutros.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 2 scripts 119 downloads 9 exports 27 dependencies

Last updated 9 months agofrom:2fdfeb0ed7. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winOKOct 30 2024
R-4.5-linuxOKOct 30 2024
R-4.4-winOKOct 30 2024
R-4.4-macOKOct 30 2024
R-4.3-winOKOct 30 2024
R-4.3-macOKOct 30 2024

Exports:accumulate.zscorescorrect.zscore.signscosine.similarity.cutoffcosine.similarity.iterativefit.and.evaluateget.qc.barplotget.qc.heatmapget.qc.multipanelplotzscores.from.metrics

Dependencies:BoutrosLab.plotting.generalclasscliclusterdeldire1071fitdistrplusgluegridExtragtablehexbininterpjpeglatticelatticeExtralifecyclelsaMASSMatrixpngproxyRColorBrewerRcppRcppEigenrlangSnowballCsurvival

Introduction to omicsQC

Rendered fromIntro_to_omicsQC.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-03-02
Started: 2024-03-02