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 (3.20)
`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, 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("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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | DifferentialExpression, GeneExpression, RNASeq, Software |
Version | 1.3.0 |
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 |
See More
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_1.3.0.tar.gz |
Windows Binary | orthos_1.3.0.zip |
macOS Binary (x86_64) | orthos_1.3.0.tgz |
macOS Binary (arm64) | orthos_1.3.0.tgz |
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 |