orthos
This is the released version of orthos; for the devel version, see orthos.
`orthos` is an R package for variance decomposition using conditional variational auto-encoders
Bioconductor version: Release (3.23)
`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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 1.10.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | MIT + file LICENSE |
| 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
Follow Installation instructions to use this package in your R session.
| Source Package | orthos_1.10.0.tar.gz |
| Windows Binary (x86_64) | orthos_1.10.0.zip |
| macOS Binary (big-sur-x86_64) | orthos_1.10.0.tgz |
| macOS Binary (sonoma-arm64) | orthos_1.10.0.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 |