Package: OncoSubtype 1.0.0
Dadong Zhang
OncoSubtype: Predict Cancer Subtypes Based on TCGA Data using Machine Learning Method
Provide functionality for cancer subtyping using nearest centroids or machine learning methods based on TCGA data.
Authors:
OncoSubtype_1.0.0.tar.gz
OncoSubtype_1.0.0.zip(r-4.5)OncoSubtype_1.0.0.zip(r-4.4)OncoSubtype_1.0.0.zip(r-4.3)
OncoSubtype_1.0.0.tgz(r-4.4-any)OncoSubtype_1.0.0.tgz(r-4.3-any)
OncoSubtype_1.0.0.tar.gz(r-4.5-noble)OncoSubtype_1.0.0.tar.gz(r-4.4-noble)
OncoSubtype_1.0.0.tgz(r-4.4-emscripten)OncoSubtype_1.0.0.tgz(r-4.3-emscripten)
OncoSubtype.pdf |OncoSubtype.html✨
OncoSubtype/json (API)
# Install 'OncoSubtype' in R: |
install.packages('OncoSubtype', repos = c('https://dadongz.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/dadongz/oncosubtype/issues
- example_fpkm - Example FPKM data
- hnsc_centroids - HNSC predictor centroids
- luad_centroids - LUAD predictor centroids
- lusc_centroids - LUSC predictor centroids
Last updated 8 months agofrom:a4a3d4ba0e. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 19 2024 |
R-4.5-win | OK | Nov 19 2024 |
R-4.5-linux | OK | Nov 19 2024 |
R-4.4-win | OK | Nov 19 2024 |
R-4.4-mac | OK | Nov 19 2024 |
R-4.3-win | OK | Nov 19 2024 |
R-4.3-mac | OK | Nov 19 2024 |
Exports:centroids_subtypeget_hvgget_median_centeredload_dataset_from_githubml_subtypePlotHeat
Dependencies:abindaskpassBiobaseBiocGenericscaretclasscliclockcodetoolscolorspacecpp11crayoncurldata.tableDelayedArraydiagramdigestdplyre1071fansifarverforeachfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2globalsgluegowergtablehardhathttripredIRangesisobanditeratorsjsonliteKernSmoothlabelinglatticelavalifecyclelimmalistenvlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimeModelMetricsmunsellnlmennetnumDerivopensslparallellypheatmappillarpkgconfigplyrpROCprodlimprogressrproxypurrrR6randomForestrbibutilsRColorBrewerRcppRdpackrecipesreshape2rlangrpartS4ArraysS4VectorsscalesshapeSparseArraySQUAREMstatmodstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimechangetimeDatetzdbUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
Help page | Topics |
---|---|
Predict the subtypes of selected cancer type based published papers | centroids_subtype |
example FPKM data | example_fpkm |
select highly variable genes from a expression matrix | get_hvg |
convert expression matrix to median-centered | get_median_centered |
Predict the subtypes of selected cancer type | get_rf_pred |
HNSC predictor centroids | hnsc_centroids |
Load Dataset from GitHub Repository | load_dataset_from_github |
LUAD predictor centroids | luad_centroids |
LUSC predictor centroids | lusc_centroids |
Predict the subtypes of selected cancer type using machine learning | ml_subtype |
Plot heatmap of the train set or test set | PlotHeat |
Set the SubtypeClass | SubtypeClass SubtypeClass-class |