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
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OncoSubtype_1.0.0.tgz(r-4.6-any)OncoSubtype_1.0.0.tgz(r-4.5-any)
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OncoSubtype_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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 stars 10 scripts 289 downloads 6 exports 93 dependencies

Last updated from:569fd49d70. Checks:9 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
linux-devel-x86_64	OK	333
source / vignettes	OK	245
linux-release-x86_64	OK	286
macos-release-arm64	OK	348
macos-oldrel-arm64	OK	259
windows-devel	OK	205
windows-release	OK	260
windows-oldrel	OK	268
wasm-release	OK	157

Exports:centroids_subtype get_hvg get_median_centered load_dataset_from_github ml_subtype PlotHeat

Dependencies:abind Biobase BiocGenerics caret class cli clock codetools cpp11 data.table DelayedArray diagram digest dplyr e1071 farver foreach future future.apply generics GenomicRanges ggplot2 globals glue gower gtable hardhat ipred IRanges isoband iterators KernSmooth labeling lattice lava lifecycle limma listenv lubridate magrittr MASS Matrix MatrixGenerics matrixStats ModelMetrics nlme nnet numDeriv parallelly pheatmap pillar pkgconfig plyr pROC prodlim progressr proxy purrr R6 randomForest rbibutils RColorBrewer Rcpp Rdpack recipes reshape2 rlang rpart S4Arrays S4Vectors S7 scales Seqinfo shape SparseArray sparsevctrs SQUAREM statmod stringi stringr SummarizedExperiment survival tibble tidyr tidyselect timechange timeDate tzdb utf8 vctrs viridisLite withr XVector

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

OncoSubtype | Installation | Example | Predict (Lung Squamous Cell Carcinoma) LUSC mRNA Expression Subtypes using wilkerson method | Using random forest model by training TCGA LUSC data | Check the consistance between two methods | Plotheat map

Rendered fromOncoSubtype.Rmdusingknitr::rmarkdown

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)