gimap
Calculate Genetic Interactions for Paired CRISPR Targets
Description
Helps find meaningful patterns in complex genetic experiments. First gimap takes data from paired CRISPR (Clustered regularly interspaced short palindromic repeats) screens that has been pre-processed to counts table of paired gRNA (guide Ribonucleic Acid) reads. The input data will have cell counts for how well cells grow (or don't grow) when different genes or pairs of genes are disabled. The output of the 'gimap' package is genetic interaction scores which are the distance between the observed CRISPR score and the expected CRISPR score. The expected CRISPR scores are what we expect for the CRISPR values to be for two unrelated genes. The further away an observed CRISPR score is from its expected score the more we suspect genetic interaction. The work in this package is based off of original research from the Alice Berger lab at Fred Hutchinson Cancer Center (2021) <doi:10.1016/j.celrep.2021.109597>.
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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 13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Jun 9, 2026
ERROR 12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE Jun 8, 2026
package dependencies
Package required but not available: ‘janitor’ See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’ manual.
OK 12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Apr 25, 2026
NOTE 11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE Mar 10, 2026
installed package size
installed size is 13.7Mb
sub-directories of 1Mb or more:
doc 3.3Mb
extdata 8.6Mb
installed package size
installed size is 13.8Mb
sub-directories of 1Mb or more:
doc 3.3Mb
extdata 8.6Mb
installed package size
installed size is 13.7Mb
sub-directories of 1Mb or more:
doc 3.3Mb
extdata 8.6Mb
Code & tests
Open call graph →Line coverage
–
Expression
–
Tests / Examples
–
Functions
39 29 exported
Complexity
4.7 avg / 25 max
Call network
39 nodes / 43 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
11,109
Files
96
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
30
Internal functions
10
Recent export changes
Testing & CI
Has tests
Yes
Test-to-code ratio
0.16
testthat edition
3
CI present
No
CI type
[]
PR gated
No
Docs
Return-value doc rate
100%
\dontrun example ratio
91.7%
Roxygen coverage
96.7%
Has pkgdown
No
NEWS present
Yes
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
20%
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
5
First release
2025-02-03
Latest release
2026-02-05
Avg cadence
36 days
Cold removal rate
100%
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/cran-code-metrics.