Package: orthos 1.10.0
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_1.10.0.tar.gz
orthos_1.10.0.zip(r-4.7)orthos_1.10.0.zip(r-4.6)orthos_1.10.0.zip(r-4.5)
orthos_1.10.0.tgz(r-4.6-any)orthos_1.10.0.tgz(r-4.5-any)
orthos_1.10.0.tar.gz(r-4.7-any)orthos_1.10.0.tar.gz(r-4.6-any)
orthos_1.10.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
orthos/json (API)
NEWS
| # Install 'orthos' in R: |
| install.packages('orthos', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:orthos-1.11.0(bioc 3.24)orthos-1.10.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
rnaseqdifferentialexpressiongeneexpression
Last updated from:cfebd32305 (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 220 | ||
| linux-devel-x86_64 | NOTE | 1547 | ||
| source / vignettes | OK | 1291 | ||
| linux-release-x86_64 | NOTE | 1626 | ||
| macos-release-arm64 | NOTE | 1111 | ||
| macos-oldrel-arm64 | NOTE | 1265 | ||
| windows-devel | NOTE | 1010 | ||
| windows-release | NOTE | 776 | ||
| windows-oldrel | NOTE | 755 | ||
| wasm-release | OK | 195 |
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 |