Package: TOP 1.5.0

Harry Robertson

TOP: TOP Constructs Transferable Model Across Gene Expression Platforms

TOP constructs a transferable model across gene expression platforms for prospective experiments. Such a transferable model can be trained to make predictions on independent validation data with an accuracy that is similar to a re-substituted model. The TOP procedure also has the flexibility to be adapted to suit the most common clinical response variables, including linear response, binomial and Cox PH models.

Authors:Harry Robertson [aut, cre], Nicholas Robertson [aut]

TOP_1.5.0.tar.gz
TOP_1.5.0.zip(r-4.5)TOP_1.5.0.zip(r-4.4)TOP_1.5.0.zip(r-4.3)
TOP_1.5.0.tgz(r-4.4-any)TOP_1.5.0.tgz(r-4.3-any)
TOP_1.5.0.tar.gz(r-4.5-noble)TOP_1.5.0.tar.gz(r-4.4-noble)
TOP_1.5.0.tgz(r-4.4-emscripten)TOP_1.5.0.tgz(r-4.3-emscripten)
TOP.pdf |TOP.html✨
TOP/json (API)

# Install 'TOP' in R:

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

Bug tracker:https://github.com/harry25r/top/issues

Datasets:

TOP_data_binary - A simulated binary data

On BioConductor:TOP-1.5.0(bioc 3.20)TOP-1.4.0(bioc 3.19)

bioconductor-package

14 exports 0.49 score 204 dependencies

Last updated 2 months agofrom:3d414c4c6e

Exports:coefNetworkPlot expit filterFeatures pairwise_col_diff performance_TOP predict_TOP ROC_Plot simplenetworkPlot Surv_TOP_CI TOP_coefPlot TOP_lambdaPlot TOP_model TOP_survival TOP_survivalPrediction

Dependencies:abind annotate AnnotationDbi askpass assertthat backports base64enc BH Biobase BiocBaseUtils BiocGenerics BiocParallel Biostrings bit bit64 blob boot broom bslib cachem calibrate car carData caret checkmate class ClassifyR cli clock cluster codetools colorspace corrplot cowplot cpp11 crayon crosstalk curl data.table DBI DelayedArray Deriv diagram digest directPA doBy doParallel dplyr e1071 ellipsis evaluate fansi farver fastmap fontawesome foreach foreign formatR Formula fs futile.logger futile.options future future.apply genefilter generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggforce ggnewscale ggplot2 ggpubr ggraph ggrepel ggsci ggsignif ggthemes ggupset glmnet globals glue gower graphlayouts gridExtra gtable hardhat highr Hmisc htmlTable htmltools htmlwidgets httr igraph ipred IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r later latex2exp lattice lava lazyeval lifecycle limma listenv lme4 lubridate magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv microbenchmark mime minqa ModelMetrics modelr MultiAssayExperiment munsell nlme nloptr nnet numDeriv openssl parallelly pbkrtest pillar pkgconfig plogr plotly plyr png polyclip polynom pROC prodlim progressr promises proxy purrr quantreg R6 ranger rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen recipes reshape2 rlang rmarkdown rpart RSQLite rstatix rstudioapi S4Arrays S4Vectors sass scales shape snow SparseArray SparseM SQUAREM statmod stringi stringr SummarizedExperiment survival sys systemfonts tibble tidygraph tidyr tidyselect timechange timeDate tinytex tweenr tzdb UCSC.utils utf8 vctrs viridis viridisLite withr xfun XML xtable XVector yaml zlibbioc

Tranferable Omics Pediction

Harry Robertson, Nicholas Robertson, Ellis Patrick

Rendered fromBuildingATOPModel.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2023-04-14
Started: 2023-01-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
coefNetworkPlot	coefNetworkPlot
The expit function	expit
filterFeatures	filterFeatures
Compute pairwise difference between matrix columns	pairwise_col_diff
performance_TOP	performance_TOP
Prectict using the Trasferable Omics Prediction model.	predict_TOP
ROC_Plot	ROC_Plot
simplenetworkPlot	simplenetworkPlot
Create a function to calculate the concordance index.	Surv_TOP_CI
TOP_coefPlot	TOP_coefPlot
A simulated binary data	TOP_data_binary
TOP_lambdaPlot	TOP_lambdaPlot
TOP_model	TOP_model
TOP_survival	TOP_survival
TOP_survivalPrediction	TOP_survivalPrediction