orthos
This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see orthos.
`orthos` is an R package for variance decomposition using conditional variational auto-encoders
Bioconductor version: 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("orthos")):
Installation
To install this package, start R (version "4.3") 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.
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 | 1.0.1 |
| In Bioconductor since | BioC 3.18 (R-4.3) (0.5 years) |
| 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_1.0.1.tar.gz |
| Windows Binary | orthos_1.0.1.zip (64-bit only) |
| macOS Binary (x86_64) | orthos_1.0.1.tgz |
| macOS Binary (arm64) | orthos_1.0.1.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 |
| Old Source Packages for BioC 3.18 | Source Archive |