Package: orthos 1.5.1
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_1.5.1.tar.gz
orthos_1.5.1.zip(r-4.5)orthos_1.5.1.zip(r-4.4)orthos_1.5.0.zip(r-4.3)
orthos_1.5.1.tgz(r-4.5-any)orthos_1.5.1.tgz(r-4.4-any)orthos_1.5.0.tgz(r-4.3-any)
orthos_1.5.1.tar.gz(r-4.5-noble)orthos_1.5.1.tar.gz(r-4.4-noble)
orthos_1.5.1.tgz(r-4.4-emscripten)orthos_1.5.0.tgz(r-4.3-emscripten)
orthos.pdf |orthos.html✨
orthos/json (API)
NEWS
| # Install 'orthos' in R: |
| install.packages('orthos', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:orthos-1.5.0(bioc 3.21)orthos-1.4.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
rnaseqdifferentialexpressiongeneexpression
Last updated 16 days agofrom:cbc0f6e2b7. Checks:1 OK, 2 FAILURE, 6 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Mar 12 2025 |
| R-4.5-win | NOTE | Mar 12 2025 |
| R-4.5-mac | NOTE | Mar 12 2025 |
| R-4.5-linux | NOTE | Mar 12 2025 |
| R-4.4-win | NOTE | Mar 12 2025 |
| R-4.4-mac | NOTE | Mar 12 2025 |
| R-4.4-linux | NOTE | Mar 12 2025 |
| R-4.3-win | OUTDATED | Jan 28 2025 |
| R-4.3-mac | OUTDATED | Dec 29 2024 |
Exports:decomposeVarloadContrastDatabaseplotQueryResultsManhplotQueryResultsViolinqueryWithContraststestOrthosEnv
Dependencies:abindAnnotationDbiAnnotationHubaskpassbackportsbase64encbasiliskbasilisk.utilsBHBiobaseBiocFileCacheBiocGenericsBiocManagerBiocParallelBiocVersionBiostringsbitbit64blobbootbroomcachemcarcarDataclicodetoolscolorspaceconfigcorrplotcowplotcpp11crayoncurlDBIdbplyrDelayedArrayDerivdir.expirydoBydplyrExperimentHubfansifarverfastmapfilelockformatRFormulafutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2ggpubrggrepelggsciggsignifgluegridExtragtableh5mreadHDF5ArrayherehttrIRangesisobandjsonliteKEGGRESTkeraslabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrmunsellnlmenloptrnnetnumDerivopensslorthosDatapbkrtestpillarpkgconfigplogrplyrpngpolynomprocessxpspurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppEigenRcppTOMLRdpackreformulasreticulaterhdf5rhdf5filtersRhdf5librlangrprojrootRSQLiterstatixrstudioapiS4ArraysS4VectorsscalessnowSparseArraySparseMstringistringrSummarizedExperimentsurvivalsystensorflowtfautographtfrunstibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewhiskerwithrXVectoryamlzeallot
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 |