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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: Development (3.20)

`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, 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>

Citation (from within R, enter citation("orthos")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

1. Introduction to orthos HTML R Script
Reference Manual PDF


biocViews DifferentialExpression, GeneExpression, RNASeq, Software
Version 1.3.0
In Bioconductor since BioC 3.18 (R-4.3) (0.5 years)
License MIT + file LICENSE
Depends R (>= 4.3), SummarizedExperiment
Imports AnnotationHub, basilisk, BiocParallel, colorspace, cowplot, DelayedArray, dplyr, ExperimentHub, ggplot2, ggpubr, ggrepel, ggsci, grDevices, grid, HDF5Array, keras, methods, orthosData, parallel, plyr, reticulate, rlang, S4Vectors, stats, tensorflow, tidyr
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Suggests BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package orthos_1.3.0.tar.gz
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macOS Binary (x86_64) orthos_1.3.0.tgz
macOS Binary (arm64) orthos_1.3.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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