orthos
This is thereleased version of orthos; for the devel version, seeorthos.
`orthos` is an R package for variance decomposition using conditional variational auto-encoders
Bioconductor version: Release (3.22)
`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: 0000-0002-1640-7636, Charlotte Soneson [aut] ORCID: 0000-0003-3833-2169, Michael Stadler [aut] ORCID: 0000-0002-2269-4934, 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 "4.5") and enter:
if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")BiocManager::install("orthos")For older versions of R, please refer to the appropriateBioconductor 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 | 1.8.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (2 years) |
| License | MIT + fileLICENSE |
| Depends | R (>= 4.3),SummarizedExperiment |
| Imports | AnnotationHub,basilisk,BiocParallel,colorspace,cowplot,DelayedArray,dplyr,ExperimentHub,ggplot2 (>= 3.4.0),ggpubr,ggrepel,ggsci, grDevices, grid,HDF5Array,keras (>= 2.16.0), 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
FollowInstallation instructions to use this package in your R session.
| Source Package | orthos_1.8.0.tar.gz |
| Windows Binary (x86_64) | orthos_1.8.0.zip |
| macOS Binary (x86_64) | orthos_1.7.4.tgz |
| macOS Binary (arm64) | orthos_1.7.4.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 |