Package: octad 1.9.0
E. Chekalin
octad: Open Cancer TherApeutic Discovery (OCTAD)
OCTAD provides a platform for virtually screening compounds targeting precise cancer patient groups. The essential idea is to identify drugs that reverse the gene expression signature of disease by tamping down over-expressed genes and stimulating weakly expressed ones. The package offers deep-learning based reference tissue selection, disease gene expression signature creation, pathway enrichment analysis, drug reversal potency scoring, cancer cell line selection, drug enrichment analysis and in silico hit validation. It currently covers ~20,000 patient tissue samples covering 50 cancer types, and expression profiles for ~12,000 distinct compounds.
Authors:
octad_1.9.0.tar.gz
octad_1.9.0.zip(r-4.5)octad_1.9.0.zip(r-4.4)octad_1.9.0.zip(r-4.3)
octad_1.9.0.tgz(r-4.4-any)octad_1.9.0.tgz(r-4.3-any)
octad_1.9.0.tar.gz(r-4.5-noble)octad_1.9.0.tar.gz(r-4.4-noble)
octad_1.9.0.tgz(r-4.4-emscripten)octad_1.9.0.tgz(r-4.3-emscripten)
octad.pdf |octad.html✨
octad/json (API)
NEWS
| # Install 'octad' in R: |
| install.packages('octad', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- res_example - Differential expression example for HCC vs adjacent liver tissue computed in diffExp() function
- sRGES_example - Data of computed example sRGEs for HCC vs liver adjacent tissues on octad.small dataset
On BioConductor:octad-1.9.0(bioc 3.21)octad-1.8.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
classificationgeneexpressionpharmacogeneticspharmacogenomicssoftwaregenesetenrichment
Last updated 3 months agofrom:33eb152a84. Checks:1 OK, 2 ERROR, 4 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Jan 14 2025 |
| R-4.5-win | ERROR | Jan 14 2025 |
| R-4.5-linux | ERROR | Jan 14 2025 |
| R-4.4-win | NOTE | Jan 14 2025 |
| R-4.4-mac | NOTE | Jan 14 2025 |
| R-4.3-win | NOTE | Jan 14 2025 |
| R-4.3-mac | NOTE | Jan 14 2025 |
Exports:computeCellLinecomputeRefTissuediffExploadOctadCountsoctadDrugEnrichmentrunsRGEStopLineEval
Dependencies:abindannotateAnnotationDbiAnnotationHubaroma.lightaskpassassortheadbase64encbeachmatBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocSingularBiocVersionbiomaRtBiostringsbitbit64bitopsblobbslibcachemclicodetoolscolorspacecpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArrayDelayedMatrixStatsdeldirDESeq2digestdplyrEDASeqedgeRevaluateExperimentHubfansifarverfastmapfilelockfontawesomeforeachformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegraphGSEABaseGSVAgtableHDF5Arrayhighrhmshtmltoolshtmlwidgetshttrhttr2hwriterinterpIRangesirlbaisobanditeratorsjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelatticeExtralazyevallifecyclelimmalocfitmagickmagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmeoctad.dbopensslpillarpkgconfigplogrplotlyplyrpngprettyunitsprogresspromisespurrrpwalignqpdfR.methodsS3R.ooR.utilsR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppGSLRcppParallelRcppZigguratRCurlreshape2restfulrRfastrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownRsamtoolsRSQLitersvdrtracklayerRUVSeqS4ArraysS4VectorssassScaledMatrixscalesShortReadSingleCellExperimentsnowSparseArraysparseMatrixStatsSpatialExperimentstatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytexUCSC.utilsutf8vctrsviridisLitewithrxfunXMLxml2xtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute Correlation between cell lines and vector of case ids. | computeCellLine |
| Compute correlating reference control samples. | computeRefTissue |
| Compute differential expression | diffExp |
| Load octad expression data | loadOctadCounts |
| Open Cancer TherApeutic Discovery (OCTAD) database package | octad |
| Compute Drug enrichment | octadDrugEnrichment |
| Differential expression example for HCC vs adjacent liver tissue computed in diffExp() function | res_example |
| Compute sRGES | runsRGES |
| Data of computed example sRGEs for HCC vs liver adjacent tissues on octad.small dataset | sRGES_example |
| Evaluate cell lines | topLineEval |
