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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: Development (3.19)

`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")):

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("orthos")

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

Documentation

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

browseVignettes("orthos")
1. Introduction to orthos HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews DifferentialExpression, GeneExpression, RNASeq, Software
Version 1.1.1
In Bioconductor since BioC 3.18 (R-4.3) (< 6 months)
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
System Requirements
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Suggests BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0)
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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package orthos_1.1.1.tar.gz
Windows Binary orthos_1.1.1.zip
macOS Binary (x86_64) orthos_1.1.1.tgz
macOS Binary (arm64)
Source Repository git clone https://git.bioconductor.org/packages/orthos
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/orthos
Bioc Package Browser https://code.bioconductor.org/browse/orthos/
Package Short Url https://bioconductor.org/packages/orthos/
Package Downloads Report Download Stats