Introduction | Installation and overview | Demonstration data | Decomposition of differential gene expression variance into specific and non-specific components using decomposeVar() | Prelude: A short overview of the orthos models | Contrast decomposition with decomposeVar() | Querying the database of gene contrasts using queryWithContrasts() | Accessing the contrast database | Advanced use cases: Directly accessing the orthos models | Session information | References
Package: orthos 1.11.1
Panagiotis Papasaikas
orthos: `orthos` is an R package for variance decomposition using conditional variational auto-encoders
`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.
Authors:
orthos_1.11.1.tar.gz
orthos_1.11.1.zip(r-4.7)orthos_1.11.1.zip(r-4.6)orthos_1.11.1.zip(r-4.5)
orthos_1.11.1.tgz(r-4.6-any)orthos_1.11.1.tgz(r-4.5-any)
orthos_1.11.1.tar.gz(r-4.7-any)orthos_1.11.1.tar.gz(r-4.6-any)
orthos_1.11.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
orthos/json (API)
| # Install 'orthos' in R: |
| install.packages('orthos', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/fmicompbio/orthos/issues
Pkgdown/docs site:https://fmicompbio.github.io
On BioConductor:orthos-1.11.0(bioc 3.24)orthos-1.10.0(bioc 3.23)
rnaseqdifferentialexpressiongeneexpression
Last updated from:cb1bea2f37. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 240 | ||
| linux-devel-x86_64 | NOTE | 2439 | ||
| source / vignettes | OK | 1495 | ||
| linux-release-x86_64 | NOTE | 2503 | ||
| macos-release-arm64 | NOTE | 1561 | ||
| macos-oldrel-arm64 | NOTE | 1751 | ||
| windows-devel | NOTE | 1522 | ||
| windows-release | NOTE | 1416 | ||
| windows-oldrel | NOTE | 1144 | ||
| wasm-release | OK | 194 |
Exports:decomposeVarloadContrastDatabaseplotQueryResultsManhplotQueryResultsViolinqueryWithContraststestOrthosEnv
Dependencies:abindAnnotationDbiAnnotationHubaskpassbackportsbase64encbasiliskBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsbiocmakeBiocManagerBiocParallelBiocVersionBiostringsbitbit64blobbootbroomcachemcarcarDataclicodetoolscolorspaceconfigcorrplotcowplotcpp11crayoncurlDBIdbplyrDelayedArrayDerivdir.expirydoBydplyrExperimentHubfarverfastmapfilelockforecastformatRFormulafracdifffutile.loggerfutile.optionsgenericsGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtableh5mreadHDF5Arrayherehttrhttr2IRangesisobandjsonliteKEGGRESTkeraslabelinglambda.rlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrnlmenloptrnnetnumDerivopensslorthosDatapbkrtestpillarpkgconfigplyrpngpolynomprocessxpspurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRcppTOMLRdpackreformulasreticulaterhdf5rhdf5filtersRhdf5librlangrprojrootRSQLiterstatixrstudioapiS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystensorflowtfautographtfrunstibbletidyrtidyselecttimeDateurcautf8vctrsviridisLitewhiskerwithrXVectoryamlzeallotzoo
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| orthos - variance decomposition using conditional variational auto-encoders | orthos-package orthos |
| Decompose input contrasts to decoded and residual fractions | decomposeVar |
| Load contrast database | loadContrastDatabase |
| Visualize query results as a composite manhattan/density plot. | plotQueryResultsManh |
| Visualize query results as violin plots | plotQueryResultsViolin |
| Query the contrast database with a set of contrasts | queryWithContrasts |
| Test conda environment | testOrthosEnv |