Description
Detects copy number alteration events in targeted exon sequencing data for tumor samples without matched normal controls. The advantage of this method is that it can be applied to smaller sequencing panels including evaluations of exon, transcript, gene, or even user specified genetic regions of interest. Functions in the package include steps for GC-content correction, calculation of quantile based normal karyotype ranges, and calculation of feature score. Cutoffs for "normal" quantile and score are user-adjustable.
Downloads
202
Last 30 days
23079th
508
Last 90 days
2.4K
Last year
Trend: +75.7% (30d vs prior 30d)
0
Last 30 days
23
Last 90 days
97
Last year
Trend: -100% (30d vs prior 30d)
3
Last 7 days
6
Last 30 days
0
All-time
autoCRAN-only: this name is served only by autoCRAN, so the count is exact.
CRAN Check Status
Show all 13 flavors
| Flavor | Status |
|---|---|
| r-devel-linux-x86_64-debian-clang | OK |
| r-devel-linux-x86_64-debian-gcc | OK |
| r-devel-linux-x86_64-fedora-clang | OK |
| r-devel-linux-x86_64-fedora-gcc | 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 History
OK 14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
Code
Structure
Lines of code
2,758
Files
35
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
7
Internal functions
14
Recent export changes
Testing & CI
Has tests
No
Test-to-code ratio
0.00
testthat edition
3
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
71.4%
\dontrun example ratio
0%
Roxygen coverage
100%
Has pkgdown
No
NEWS present
Yes
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
0%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
1
First release
2024-12-03
Latest release
2024-12-03
Avg cadence
–
Cold removal rate
–
Dep drift
0
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.
Dependency Network
Version History
1 trackedR Observatory began tracking this package on Mar 10, 2026; it first appeared on CRAN Dec 3, 2024. Releases before tracking aren’t shown.