Package: sigminer.prediction 0.2.0

sigminer.prediction: Train and Predict Cancer Subtype with Keras Model based on Mutational Signatures

Mutational signatures represent mutational processes occured in cancer evolution, thus are stable and genetic resources for subtyping. This tool provides functions for training neutral network models to predict the subtype a sample belongs to based on 'keras' and 'sigminer' packages.

Authors:Shixiang Wang [aut, cre]

sigminer.prediction_0.2.0.tar.gz
sigminer.prediction_0.2.0.zip(r-4.5)sigminer.prediction_0.2.0.zip(r-4.4)sigminer.prediction_0.2.0.zip(r-4.3)
sigminer.prediction_0.2.0.tgz(r-4.4-any)sigminer.prediction_0.2.0.tgz(r-4.3-any)
sigminer.prediction_0.2.0.tar.gz(r-4.5-noble)sigminer.prediction_0.2.0.tar.gz(r-4.4-noble)
sigminer.prediction_0.2.0.tgz(r-4.4-emscripten)sigminer.prediction_0.2.0.tgz(r-4.3-emscripten)
sigminer.prediction.pdf |sigminer.prediction.html✨
sigminer.prediction/json (API)

# Install 'sigminer.prediction' in R:

install.packages('sigminer.prediction', repos = c('https://shixiangwang.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/shixiangwang/sigminer.prediction/issues

On CRAN:

keras mutational-signatures prostate-cancer sigminer

7 exports 8 stars 0.91 score 136 dependencies

Last updated 2 years agofrom:0572bfc65f

Exports:batch_modeling_and_fitting copy_model list_trained_models load_trained_model modeling_and_fitting prepare_data tidy

Dependencies:abind backports base64enc Biobase BiocGenerics BiocManager boot broom car carData caret class cli clock cluster codetools colorspace config corrplot cowplot cpp11 data.table Deriv diagram digest DNAcopy doBy doParallel dplyr e1071 fansi farver foreach furrr future future.apply generics ggplot2 ggpubr ggrepel ggsci ggsignif globals glue gower gridBase gridExtra gtable hardhat here ipred isoband iterators jsonlite keras KernSmooth labeling lattice lava lifecycle listenv lme4 lubridate maftools magrittr MASS Matrix MatrixModels mgcv microbenchmark minqa ModelMetrics modelr munsell nlme nloptr NMF nnet numDeriv parallelly pbkrtest pillar pkgconfig plyr png polynom pROC processx prodlim progressr proxy ps purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen RcppTOML recipes registry reshape2 reticulate Rhtslib rlang rngtools rpart rprojroot rstatix rstudioapi scales shape sigminer SparseM SQUAREM stringi stringr survival tensorflow tfautograph tfruns tibble tidyr tidyselect timechange timeDate tzdb utf8 vctrs viridisLite whisker withr yaml zeallot zlibbioc

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Construct A Batch of Keras Models	batch_modeling_and_fitting
Copy Model File	copy_model
List Current Available Trained Keras Models	list_trained_models
Load Trained Models	load_trained_model
Create 5-layer Keras Model and Fitting Datasets	modeling_and_fitting
Prepare Training and Test Dataset	prepare_data
Tidy Modeling Result	tidy