This is the released version of orthos; for the devel version, see orthos.
`orthos` is an R package for variance decomposition using conditional variational auto-encodersBioconductor version: Release (3.21)
`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] ORCID: 0000-0002-1640-7636 , Charlotte Soneson [aut] ORCID: 0000-0003-3833-2169 , Michael Stadler [aut] ORCID: 0000-0002-2269-4934 , Friedrich Miescher Institute for Biomedical Research [cph]
Maintainer: Panagiotis Papasaikas <panagiotis.papasaikas at fmi.ch>
Citation (from within R, entercitation("orthos")): Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("orthos")
For older versions of R, please refer to the appropriate Bioconductor release.
DocumentationTo view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("orthos")Follow Installation instructions to use this package in your R session.
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