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OmicsQC

Nominating Quality Control Outliers in Genomic Profiling Studies

v1.1.1 · Jan 23, 2026 · GPL-2

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.

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CRAN Check Status

1 ERROR
13 OK
Show all 14 flavors
Flavor Status
r-devel-linux-x86_64-debian-clang OK
r-devel-linux-x86_64-debian-gcc ERROR
r-devel-linux-x86_64-fedora-clang OK
r-devel-linux-x86_64-fedora-gcc OK
r-devel-macos-arm64 OK
r-devel-windows-x86_64 OK
r-oldrel-macos-arm64 OK
r-oldrel-macos-x86_64 OK
r-oldrel-windows-x86_64 OK
r-patched-linux-x86_64 OK
r-release-linux-x86_64 OK
r-release-macos-arm64 OK
r-release-macos-x86_64 OK
r-release-windows-x86_64 OK
Check details (14 non-OK)
OK r-devel-linux-x86_64-debian-clang

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ERROR r-devel-linux-x86_64-debian-gcc

tests

  Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat);
  > 
  > test_check('OmicsQC')
  Loading required package: OmicsQC
  Saving _problems/test-plotting-127.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 66 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plotting.R:124:3'): get.qc.multipanelplot ────────────────────
  Expected `get.qc.multipanelplot(barplot = bp, heatmap = hm)` not to throw any errors.
  Actually got a <simpleError> with message:
    a character vector argument expected
  Backtrace:
       ▆
    1. ├─testthat::expect_error(...) at test-plotting.R:124:3
    2. │ └─testthat:::expect_condition_matching_(...)
    3. │   └─testthat:::quasi_capture(...)
    4. │     ├─testthat (local) .capture(...)
    5. │     │ └─base::withCallingHandlers(...)
    6. │     └─rlang::eval_bare(quo_get_expr(.quo), quo_get_env(.quo))
    7. └─OmicsQC::get.qc.multipanelplot(barplot = bp, heatmap = hm)
    8.   └─BoutrosLab.plotting.general::create.multipanelplot(...)
    9.     └─BoutrosLab.plotting.general:::get.legend.height(...)
   10.       └─tools::file_ext(filename)
   11.         ├─base::ifelse(...)
   12.         ├─base::grepl("^(.*[^.]+.*)[.]([[:alnum:]]+)$", basename(x))
   13.         │ └─base::is.factor(x)
   14.         └─base::basename(x)
  
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 66 ]
  Error:
  ! Test failures.
  Execution halted
OK r-devel-linux-x86_64-fedora-clang

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OK r-devel-linux-x86_64-fedora-gcc

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OK r-devel-macos-arm64

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OK r-devel-windows-x86_64

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OK r-oldrel-macos-arm64

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OK r-oldrel-macos-x86_64

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OK r-oldrel-windows-x86_64

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OK r-patched-linux-x86_64

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OK r-release-linux-x86_64

*


            
OK r-release-macos-arm64

*


            
OK r-release-macos-x86_64

*


            
OK r-release-windows-x86_64

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Check History

ERROR 13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Mar 9, 2026
ERROR r-devel-linux-x86_64-debian-gcc

tests

  Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat);
  > 
  > test_check('OmicsQC')
  Loading required package: OmicsQC
  Saving _problems/test-plotting-127.R
  [ FAIL 1 | WARN 0 | SKIP 0 | PASS 66 ]
  
  ══ Failed tests ════════════════════════════════════════════════════════════════
  ── Failure ('test-plotting.R:124:3'): get.qc.multipanelplot ────────────────────
  Expected `get.qc.multipanelplot(barplot = bp, heatmap = hm)` no

Dependency Network

Dependencies Reverse dependencies fitdistrplus lsa BoutrosLab.plotting.general OmicsQC

Version History

new 1.1.1 Mar 9, 2026