Package: OmicsQC
Type: Package
Title: Nominating Quality Control Outliers in Genomic Profiling Studies
Version: 1.1.1
Authors@R: 
    c(
    person(given = "Anders Hugo",
           family = "Frelin",
           email = "ahfrelin@g.ucla.edu",
           role = c("aut")),
    person(given = "Helen",
           family = "Zhu",
           role = c("aut"),
           email = "helen.zhu@mail.utoronto.ca"),
    person(given = "Paul C.",
           family = "Boutros",
           role = c("aut", "cre"),
           email = "PBoutros@sbpdiscovery.org",
           comment = c(ORCID = "0000-0003-0553-7520"))
    )
Description: 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.
Depends: R (>= 2.10)
Imports: stats, utils, fitdistrplus, lsa, BoutrosLab.plotting.general
Suggests: knitr, rmarkdown, kableExtra, dplyr, testthat (>= 3.0.0)
Config/testthat/edition: 3
License: GPL-2
Encoding: UTF-8
LazyData: true
VignetteBuilder: knitr
RoxygenNote: 7.2.3
NeedsCompilation: no
Packaged: 2026-01-23 22:27:20 UTC; rhughwhite
Author: Anders Hugo Frelin [aut],
  Helen Zhu [aut],
  Paul C. Boutros [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-0553-7520>)
Maintainer: Paul C. Boutros <PBoutros@sbpdiscovery.org>
Repository: CRAN
Date/Publication: 2026-01-24 00:20:08 UTC
Built: R 4.7.0; ; 2026-08-04 03:07:21 UTC; windows
