denovolyzeR
Statistical Analyses of De Novo Genetic Variants
Description
An integrated toolset for the analysis of de novo (sporadic) genetic sequence variants. denovolyzeR implements a mutational model that estimates the probability of a de novo genetic variant arising in each human gene, from which one can infer the expected number of de novo variants in a given population size. Observed variant frequencies can then be compared against expectation in a Poisson framework. denovolyzeR provides a suite of functions to implement these analyses for the interpretation of de novo variation in human disease.
Downloads
285
Last 30 days
16710th
667
Last 90 days
2.8K
Last year
Trend: +83.9% (30d vs prior 30d)
0
Last 30 days
25
Last 90 days
117
Last year
Trend: -100% (30d vs prior 30d)
6
Last 7 days
17
Last 30 days
2
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 | 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)
CRAN incoming feasibility
Maintainer: ‘James Ware <j.ware@imperial.ac.uk>’
Found the following URLs which should use \doi (with the DOI name only):
File ‘fmrpGenes.Rd’:
http://dx.doi.org/10.1016/j.cell.2011.06.013
CRAN incoming feasibility
Maintainer: ‘James Ware <j.ware@imperial.ac.uk>’
Found the following URLs which should use \doi (with the DOI name only):
File ‘fmrpGenes.Rd’:
http://dx.doi.org/10.1016/j.cell.2011.06.013
Check History
NOTE 11 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026
CRAN incoming feasibility
Maintainer: ‘James Ware <j.ware@imperial.ac.uk>’
Found the following URLs which should use \doi (with the DOI name only):
File ‘fmrpGenes.Rd’:
http://dx.doi.org/10.1016/j.cell.2011.06.013
CRAN incoming feasibility
Maintainer: ‘James Ware <j.ware@imperial.ac.uk>’
Found the following URLs which should use \doi (with the DOI name only):
File ‘fmrpGenes.Rd’:
http://dx.doi.org/10.1016/j.cell.2011.06.013
ERROR 11 OK · 1 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026
CRAN incoming feasibility
Maintainer: ‘James Ware <j.ware@imperial.ac.uk>’
Found the following URLs which should use \doi (with the DOI name only):
File ‘fmrpGenes.Rd’:
http://dx.doi.org/10.1016/j.cell.2011.06.013
CRAN incoming feasibility
Maintainer: ‘James Ware <j.ware@imperial.ac.uk>’
Found the following URLs which should use \doi (with the DOI name only):
File ‘fmrpGenes.Rd’:
http://dx.doi.org/10.1016/j.cell.2011.06.013
NOTE 12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
CRAN incoming feasibility
Maintainer: ‘James Ware <j.ware@imperial.ac.uk>’
Found the following URLs which should use \doi (with the DOI name only):
File ‘fmrpGenes.Rd’:
http://dx.doi.org/10.1016/j.cell.2011.06.013
CRAN incoming feasibility
Maintainer: ‘James Ware <j.ware@imperial.ac.uk>’
Found the following URLs which should use \doi (with the DOI name only):
File ‘fmrpGenes.Rd’:
http://dx.doi.org/10.1016/j.cell.2011.06.013
Code & tests
Open call graph →Line coverage
–
Expression
–
Tests / Examples
–
Functions
7 5 exported
Complexity
6.1 avg / 15 max
Call network
7 nodes / 4 edges
Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.
Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
1,173
Files
29
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
5
Internal functions
2
Recent export changes
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
66.7%
\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
100%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.1.0
System requirements
–
C++ standard
–
License
GPL-3
License flags
SPDX valid, OSI approved
History
Versions
3
First release
2015-04-01
Latest release
2016-08-01
Avg cadence
244 days
Cold removal rate
–
Dep drift
2
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.