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CINmetrics

Calculate Chromosomal Instability Metrics

v0.1.0 · Aug 2, 2021 · GPL-3
CRAN GitHub Mirror

Description

Implement various chromosomal instability metrics. 'CINmetrics' (Chromosomal INstability metrics) provides functions to calculate various chromosomal instability metrics on masked Copy Number Variation(CNV) data at individual sample level. The chromosomal instability metrics have been implemented as described in the following studies: Baumbusch LO et al. 2013 <doi:10.1371/journal.pone.0054356>, Davidson JM et al. 2014 <doi:10.1371/journal.pone.0079079>, Chin SF et al. 2007 <doi:10.1186/gb-2007-8-10-r215>.

Downloads

CRAN

246

Last 30 days

20177th

590

Last 90 days

2.4K

Last year

Trend: +87.8% (30d vs prior 30d)

r2u CRAN

0

Last 30 days

28

Last 90 days

113

Last year

Trend: -100% (30d vs prior 30d)

autoCRAN

2

Last 7 days

5

Last 30 days

0

All-time

autoCRAN-only: this name is served only by autoCRAN, so the count is exact.

CRAN Check Status

2 NOTE
11 OK
Show all 13 flavors
Flavor Status
r-devel-linux-x86_64-debian-clang NOTE
r-devel-linux-x86_64-debian-gcc NOTE
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 details (2 non-OK)
NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Vishal H. Oza <vishoza@uab.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Vishal", "H."),
                      family = "Oza",
                      role = c("aut", "cre"),
                      email = "vishoza@uab.edu"),
               person(given = "Roshan",
                      family = "Darji",
                      role = "aut"),
               person(given = c("Brittany", "N."),
                      family = "Lasseigne",
                      role = "aut"))
as necessary.
NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Vishal H. Oza <vishoza@uab.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Vishal", "H."),
                      family = "Oza",
                      role = c("aut", "cre"),
                      email = "vishoza@uab.edu"),
               person(given = "Roshan",
                      family = "Darji",
                      role = "aut"),
               person(given = c("Brittany", "N."),
                      family = "Lasseigne",
                      role = "aut"))
as necessary.

Check History

NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
NOTE r-devel-linux-x86_64-debian-clang

CRAN incoming feasibility

Maintainer: ‘Vishal H. Oza <vishoza@uab.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Vishal", "H."),
                      family = "Oza",
                      role = c("aut", "cre"),
         
...[truncated]...
   person(given = "Roshan",
                      family = "Darji",
                      role = "aut"),
               person(given = c("Brittany", "N."),
                      family = "Lasseigne",
                      role = "aut"))
as necessary.
NOTE r-devel-linux-x86_64-debian-gcc

CRAN incoming feasibility

Maintainer: ‘Vishal H. Oza <vishoza@uab.edu>’

No Authors@R field in DESCRIPTION.
Please add one, modifying
  Authors@R: c(person(given = c("Vishal", "H."),
                      family = "Oza",
                      role = c("aut", "cre"),
         
...[truncated]...
   person(given = "Roshan",
                      family = "Darji",
                      role = "aut"),
               person(given = c("Brittany", "N."),
                      family = "Lasseigne",
                      role = "aut"))
as necessary.

Code & tests

Open call graph →

Line coverage

–

Expression

–

Tests / Examples

–

Functions

7 7 exported

Complexity

3.1 avg / 6 max

Call network

7 nodes / 5 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

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Lowest coverage

Per-function coverage is not measured for this package yet.

Code

Structure

Lines of code

736

Files

20

Compiled share

0%

Has compiled src

No

Language breakdown

R 289 (39.3%)Docs 294 (39.9%)Vignettes 153 (20.8%)

API

Exported functions

7

Internal functions

0

Recent export changes

v0.1.0+7 CINmetrics, cna, countingBaseSegments +4 more

Testing & CI

Has tests

No

Test-to-code ratio

0.00

testthat edition

–

CI present

No

CI type

[]

PR gated

No

Docs

Return-value doc rate

100%

\dontrun example ratio

0%

Roxygen coverage

100%

Has pkgdown

No

NEWS present

No

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

2.10

System requirements

–

C++ standard

–

License

GPL-3

License flags

SPDX valid, OSI approved

History

Versions

1

First release

2021-08-02

Latest release

2021-08-02

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.

Version History

1 tracked
new 0.1.0 Mar 10, 2026

R Observatory began tracking this package on Mar 10, 2026; it first appeared on CRAN Aug 2, 2021. Releases before tracking aren’t shown.