DECIPHER
Bioc currentTools for curating, analyzing, and manipulating biological sequences
Release Lineage
Entered 2.9 · Nov 1, 2011
Current · Requires R 4.6
Description
A toolset for deciphering and managing biological sequences.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
366 67 exported
Complexity
42.7 avg / 443 max
Call network
366 nodes / 544 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
81,808
Files
283
Compiled share
40.7%
Has compiled src
Yes
Language breakdown
API
Exported functions
69
Internal functions
68
Recent export changes
Testing
Has tests
No
Test-to-code ratio
0.00
testthat edition
–
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
25.9%
Unsafe pattern score
78
Dep constraint coverage
14.3%
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
30
First release
2011-10-31
Latest release
2026-07-30
Avg cadence
184 days
Cold removal rate
100%
Dep drift
7
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 90includes a package overview page
- Examples that run
- 100%89 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 98%
- Return-value docs
- 97%
- Help pages citing references
- 59%
- The Art of Multiple Sequence Alignment in R PDF
- Classify Sequences in R PDF
- Upsize Your Clustering with Clusterize PDF
- Getting Started DECIPHERing PDF
- Design Microarray Probes in R PDF
- Design Group-Specific Primers in R PDF
- Design Group-Specific FISH Probes in R PDF
- Design Primers that Yield Group-Specific Signatures PDF
- Finding Chimeric Sequences in R PDF
- The Magic of Gene Finding PDF
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 |
|---|---|---|---|
| BLOSUM | array | 24 × 24 × 15 | No other package |
| HEC_MI1 | array | 20 × 21 × 3 | No other package |
| HEC_MI2 | array | 20 × 20 × 21 × 21 × 3 | No other package |
| MIQS | matrix | 25 × 25 | No other package |
| MMLSUM | array | 21 × 21 × 9 | No other package |
| NonCodingRNA_Archaea | list | 26 elements | No other package |
| NonCodingRNA_Bacteria | list | 46 elements | No other package |
| NonCodingRNA_Eukarya | list | 33 elements | No other package |
| PAM | array | 24 × 24 × 50 | No other package |
| PFASUM | array | 25 × 25 × 90 | No other package |
| RESTRICTION_ENZYMES | vector | 214 elements | No other package |
| TrainingSet_16S | Taxa | 15 elements | No other package |
| deltaGrules | array | 5 × 5 × 5 × 5 × 5 × 5 × 5 × 5 | No other package |
| deltaGrulesRNA | array | 5 × 5 × 5 × 5 × 5 × 5 × 5 × 5 | No other package |
| deltaHrules | array | 5 × 5 × 5 × 5 × 5 × 5 × 5 × 5 | No other package |
| deltaHrulesRNA | array | 5 × 5 × 5 × 5 × 5 × 5 × 5 × 5 | No other package |
| deltaSrules | array | 5 × 5 × 5 × 5 × 5 × 5 × 5 × 5 | No other package |
| deltaSrulesRNA | array | 5 × 5 × 5 × 5 × 5 × 5 × 5 × 5 | No other package |
Topics
Depended on by (14)
Show all 17 packagesHide all 17 packages
Bioconductor (9)
CRAN (5)
Suggested by (3)
People (from the free-text Author field)
Cite
Cite this package
Run in R for the authors' entry:
citation("DECIPHER")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 v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.