deconvR
Bioc currentSimulation and Deconvolution of Omic Profiles
Release Lineage
Entered 3.14 · Oct 27, 2021
Current · Requires R 4.6
Description
This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
9 4 exported
Complexity
9.2 avg / 23 max
Call network
9 nodes / 5 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
2,259
Files
31
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
4
Internal functions
5
Testing
Has tests
Yes
Test-to-code ratio
0.81
testthat edition
3
Docs
Roxygen coverage
100%
Health & Security signals
Informational signals; not verdicts.
on.exit coverage
0%
Unsafe pattern score
0
Dep constraint coverage
71.4%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.1
System requirements
–
C++ standard
–
License
Artistic-2.0
License flags
SPDX valid, OSI approved
History
Versions
10
First release
2021-10-28
Latest release
2026-04-28
Avg cadence
182 days
Cold removal rate
–
Dep drift
1
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 6
- Examples that run
- 100%4 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 100%
- Return-value docs
- 100%
- Help pages citing references
- 50%
- deconvRVignette HTML
Repository practices
6 development-tooling and community-health practices detected across 3 families in the upstream repository
Checks run against github.com/bimsbbioinfo/deconvr on 2026-10-22.
The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel
GitHub Pages site last deployed 2026-07-22
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| HumanCellTypeMethAtlas | data.frame | 6,105 × 26 | No other package |
| IlluminaMethEpicB5ProbeIDs | – | – | – |
| WGBS_GRanges | – | – | – |
Topics
People
- Irem B. Gündüz author maintainer
- Altuna Akalin author
- Veronika Ebenal author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("deconvR")The package provides a citation file that builds its entry when R runs it. Run citation() to see it.
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.