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 (3.21)

`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: ), Charlotte Soneson [aut] (ORCID: ), Michael Stadler [aut] (ORCID: ), 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 "4.5") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DifferentialExpression, GeneExpression, RNASeq, Software
Version	1.5.0
In Bioconductor since	BioC 3.18 (R-4.3) (1 year)
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
URL

Suggests	BiocManager, BiocStyle, htmltools, knitr, rmarkdown, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

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

Source Package	orthos_1.5.0.tar.gz
Windows Binary (x86_64)	orthos_1.5.0.zip
macOS Binary (x86_64)	orthos_1.5.0.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