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:Dadong Zhang <[email protected]>

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

Datasets:

example_fpkm - Example FPKM data
hnsc_centroids - HNSC predictor centroids
luad_centroids - LUAD predictor centroids
lusc_centroids - LUSC predictor centroids

On CRAN:

3.70 score 1 scripts 114 downloads 6 exports 106 dependencies

Last updated 8 months agofrom:a4a3d4ba0e. Checks:OK: 6 WARNING: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 31 2024
R-4.5-win	OK	Oct 31 2024
R-4.5-linux	WARNING	Oct 31 2024
R-4.4-win	OK	Oct 31 2024
R-4.4-mac	OK	Oct 31 2024
R-4.3-win	OK	Oct 31 2024
R-4.3-mac	OK	Oct 31 2024

Exports:centroids_subtype get_hvg get_median_centered load_dataset_from_github ml_subtype PlotHeat

Dependencies:abind askpass Biobase BiocGenerics caret class cli clock codetools colorspace cpp11 crayon curl data.table DelayedArray diagram digest dplyr e1071 fansi farver foreach future future.apply generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 globals glue gower gtable hardhat httr ipred IRanges isoband iterators jsonlite KernSmooth labeling lattice lava lifecycle limma listenv lubridate magrittr MASS Matrix MatrixGenerics matrixStats mgcv mime ModelMetrics munsell nlme nnet numDeriv openssl parallelly pheatmap pillar pkgconfig plyr pROC prodlim progressr proxy purrr R6 randomForest rbibutils RColorBrewer Rcpp Rdpack recipes reshape2 rlang rpart S4Arrays S4Vectors scales shape SparseArray SQUAREM statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timechange timeDate tzdb UCSC.utils utf8 vctrs viridisLite withr XVector zlibbioc

Predict cancer subtypes using NCC or machine learning methods based on TCGA data

Dadong Zhang

Rendered fromOncoSubtype.Rmdusingknitr::rmarkdownon Oct 31 2024.

Last update: 2024-03-22
Started: 2024-03-22

Citation

Development and contributors

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

Usage by other packages (reverse dependencies)