orthos
This is the development version of orthos; for the stable release version, see orthos.
`orthos` is an R package for variance decomposition using conditional variational auto-encoders
Bioconductor version: 3.24 · Package version: 1.11.1
`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.
Author: Panagiotis Papasaikas [aut, cre] 
, Charlotte Soneson [aut] , Michael Stadler [aut] , Friedrich Miescher Institute for Biomedical Research [cph]
Maintainer: Panagiotis Papasaikas <panagiotis.papasaikas at fmi.ch>
Citation
From within R, enter citation("orthos"):
Panagiotis Papasaikas, Charlotte Soneson, Michael Stadler. orthos: `orthos` is an R package for variance decomposition using conditional variational auto-encoders. doi:10.18129/B9.bioc.orthos, R package version 1.11.1, https://bioconductor.org/packages/orthos.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("orthos")For older versions of R, please refer to the appropriate Bioconductor release.
Details
| Version | 1.11.1 |
| License | MIT + file LICENSE |
| URL | https://github.com/fmicompbio/orthos https://fmicompbio.github.io/orthos |
| Bug Reports | https://github.com/fmicompbio/orthos/issues |
| Last updated | 2026-06-15 |
| In Bioconductor since | BioC 3.18 (R-4.3) (2 years) |
| Downloads rank | 1752 of 2,456 |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, GeneExpression, RNASeq, Software |
| Package Short Url | https://bioconductor.org/packages/orthos/ |
Documentation
| Reference Manual | |
| NEWS | Text |
Download
Follow the installation instructions to use this package in your R session.
| Source package | orthos_1.11.1.tar.gz |
| Windows binary (x86_64) | orthos_1.11.1.zip |
| macOS binary (arm64) | orthos_1.11.1.tgz |
| macOS binary (x86_64) | orthos_1.11.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/orthos |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/orthos |
| Package Downloads Report | Download Stats |
Dependencies
Depends: R (>= 4.3), SummarizedExperiment
Imports: AnnotationHub, basilisk, BiocParallel, colorspace, cowplot, DelayedArray, dplyr, ExperimentHub, ggplot2 (>= 3.4.0), ggpubr, ggrepel, ggsci, grDevices, grid, HDF5Array, keras (>= 2.16.0), methods, orthosData, parallel, plyr, reticulate, rlang, S4Vectors, stats, tensorflow, tidyr
Suggests: BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0)