amplican
Bioc currentAutomated analysis of CRISPR experiments
Release Lineage
Entered 3.6 · Oct 31, 2017
Current · Requires R 4.6
Description
`amplican` performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
89 30 exported
Complexity
4 avg / 46 max
Call network
89 nodes / 116 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
12,512
Files
155
Compiled share
1.1%
Has compiled src
Yes
Language breakdown
API
Exported functions
53
Internal functions
51
Recent export changes
Testing
Has tests
Yes
Test-to-code ratio
0.30
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
50%
Unsafe pattern score
0
Dep constraint coverage
84%
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
18
First release
2017-10-30
Latest release
2026-04-28
Avg cadence
185 days
Cold removal rate
100%
Dep drift
12
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 75 (42 internal)includes a package overview page
- Examples that run
- 100%48 run in a plain check
- Exported functions with examples
- 89%
- Documented parameters
- 98%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
1 development-tooling and community-health practice detected across 1 family in the upstream repository
Checks run against github.com/valenlab/amplican on 2026-10-11.
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| RunParameters | – | – | – |
| barcode_reads_filters | data.frame | 2 × 10 | No other package |
| config | data.frame | 5 × 12 | No other package |
| config_summary | data.frame | 5 × 24 | No other package |
| events_filtered_shifted | data.frame | 83 × 14 | No other package |
| events_filtered_shifted_normalized | data.frame | 83 × 14 | No other package |
| experiment_data | data.frame | 5 × 21 | No other package |
| raw_events | data.frame | 94 × 12 | No other package |
| unassigned_reads | data.frame | 4 × 10 | No other package |
Topics
People
- Eivind Valen copyright holder maintainer
- Kornel Labun author
Cite
Cite this package
Run in R for the authors' entry:
citation("amplican")The package provides a citation file, so citation() returns the authors' own entry.
It points to 10.1101/gr.244293.118.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.