orthos
Bioc current`orthos` is an R package for variance decomposition using conditional variational auto-encoders
Release Lineage
Entered 3.18 · Oct 25, 2023
Current · Requires R 4.6
Description
`orthos` decomposes RNA-seq contrasts, for example obtained from a gene knock-out or compound treatment experiment, into unspecific and experiment-specific components. Original and decomposed contrasts can be efficiently queried against a large database of contrasts (derived from ARCHS4, https://maayanlab.cloud/archs4/) to identify similar experiments. `orthos` furthermore provides plotting functions to visualize the results of such a search for similar contrasts.
None published for Bioconductor
Test coverage
Line coverage
–
Expression
–
Tests / Examples
–
Functions
20 6 exported
Complexity
5.6 avg / 40 max
Call network
20 nodes / 26 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
3,467
Files
37
Compiled share
0%
Has compiled src
No
Language breakdown
API
Exported functions
6
Internal functions
14
Testing
Has tests
Yes
Test-to-code ratio
0.41
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
7.4%
Secret pattern count
0
Bundled 3rd-party code
2 items
Portability & License
Min R version
4.3
System requirements
–
C++ standard
–
License
MIT + file LICENSE
License flags
SPDX valid, OSI approved
History
Versions
6
First release
2023-11-02
Latest release
2026-04-28
Avg cadence
181 days
Cold removal rate
–
Dep drift
0
LOC over versions
Per-file churn detail lives in the source pipeline: https://github.com/r-observatory/bioc-code-metrics.
Documentation
- Help pages
- 7includes a package overview page
- Examples that run
- 100%6 run in a plain check
- Exported functions with examples
- 100%
- Documented parameters
- 93%
- Return-value docs
- 100%
- Help pages citing references
- 0%
Repository practices
Checks read the Bioconductor git repository (git.bioconductor.org), branch RELEASE_3_23.
3 practices detected in the Bioconductor git repository
Datasets
| Name | Class | Size | Also in |
|---|---|---|---|
| GSE215150_MKL1_Human | matrix | 59,453 × 3 | No other package |
| GSE215150_MKL1_Mouse | matrix | 55,367 × 3 | No other package |
Topics
People
- Panagiotis Papasaikas author maintainer
- Friedrich Miescher Institute for Biomedical Research copyright holder
- Charlotte Soneson author
- Michael Stadler author
Cite
Cite this package
Run in R for the authors' preferred citation:
citation("orthos")This package has no citation file, so citation() returns this entry built from DESCRIPTION.
Cite the R Observatory
For a number measured here: a download total, a coverage figure, an archival date.
From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.