GUIDEseq
Bioc currentGUIDE-seq and PEtag-seq analysis pipeline
Release Lineage
Entered 3.2 · Oct 14, 2015
Current · Requires R 4.6
Description
The package implements GUIDE-seq and PEtag-seq analysis workflow including functions for filtering UMI and reads with low coverage, obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites with mismatches and indels.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
38 15 exported
Complexity
9.6 avg / 52 max
Call network
38 nodes / 25 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
9,953
Files
99
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
15
Internal functions
19
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.21
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
–
Unsafe pattern score
0
Dep constraint coverage
10%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
3.5.0
System requirements
–
C++ standard
–
License
GPL (>= 2)
License flags
SPDX valid, OSI approved
History
Versions
22
First release
2015-10-28
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
20
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 20includes a package overview page
- Examples that run
- 100%18 run in a plain check (12 of them under a condition)
- Exported functions with examples
- 93%
- Documented parameters
- 91%
- Return-value docs
- 80%
- Help pages citing references
- 45%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
No development-tooling practices detected in the Bioconductor git repository.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| 1450peakSeq | – | – | – |
| InsertionInOfftarget | list | 3 elements | No other package |
| PEtagAnalysis_testthat | list | 6 elements | No other package |
| UMI-HEK293_site4_R1 | data.frame | 5,571 × 3 | No other package |
| UMI-HEK293_site4_chr13 | data.frame | 30,096 × 3 | No other package |
| alns | data.frame | 2 × 21 | 2 packages |
| both.runsum | – | – | – |
| cleavages_testthat | list | 7 elements | No other package |
| consecutiveDNABulge | data.frame | 1 × 19 | No other package |
| consecutiveDNABulge2 | data.frame | 1 × 19 | No other package |
| mergedOffTargets | data.frame | 109 × 30 | No other package |
| pa.f | list | 123 elements | No other package |
| pa.r | list | 123 elements | No other package |
| peaks | – | – | – |
| peaks.gr | – | – | – |
| subjects2 | – | – | – |
| testCFDscoringWithBulge | data.frame | 2 × 29 | No other package |
| uniqueCleavageEvents | list | 6 elements | No other package |
Topics
Depended on by (1)
Bioconductor (1)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("GUIDEseq")The package provides a citation file, so citation() returns the authors' own entry.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.