CrispRVariants
Bioc currentTools for counting and visualising mutations in a target location
Release Lineage
Entered 3.3 · May 4, 2016
Current · Requires R 4.6
Description
CrispRVariants provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
50 3 exported
Complexity
3.9 avg / 13 max
Call network
50 nodes / 26 edges
Test coverage is not measured for Bioconductor packages; nodes fall back to a neutral fill.
Call graph
Open call graph →Lowest coverage
Per-function coverage is not measured for this package yet.
Code
Structure
Lines of code
11,023
Files
133
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
24
Internal functions
47
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.08
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
12.5%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3.0
System requirements
–
C++ standard
–
License
GPL-2
License flags
SPDX valid, OSI approved
History
Versions
21
First release
2016-05-15
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 50
- Examples that run
- 96%22 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran)
- Exported functions with examples
- 90%
- Documented parameters
- 100%
- Return-value docs
- 90%
- Help pages citing references
- 0%
- CrispRVariants PDF
- CrispRVariants HTML
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
1 practice detected in the Bioconductor git repository
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| gol | – | – | – |
| gol_F1_metadata | data.frame | 24 × 3 | No other package |
| gol_F1_metadata_small | data.frame | 8 × 3 | No other package |
| reference | – | – | – |
Topics
People
- Helen Lindsay author maintainer
Cite
Cite this package
Run in R for the authors' entry:
citation("CrispRVariants")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1038/nbt.3628.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.