This site is a development preview. As such the content and styling may not be final and is subject to change before going into production. To see more information about the redesign click here.

Menu

Documentation:

R / CRAN packages and documentation

Support

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

orthos

This is the development version of orthos; to use it, please install the devel version of Bioconductor.

`orthos` is an R package for variance decomposition using conditional variational auto-encoders

Bioconductor version: Development (3.18)

`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 "4.3") 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

Reference Manual PDF

Details

biocViews DifferentialExpression, GeneExpression, RNASeq, Software
Version 0.99.1
In Bioconductor since BioC 3.18 (R-4.3)
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
Linking To
Suggests BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0)
System Requirements
Enhances
URL
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
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
Package Short Url https://bioconductor.org/packages/orthos/
Package Downloads Report Download Stats