Package: TOP 1.13.0

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_1.13.0.tar.gz
TOP_1.13.0.zip(r-4.7)TOP_1.13.0.zip(r-4.6)TOP_1.13.0.zip(r-4.5)
TOP_1.13.0.tgz(r-4.6-any)TOP_1.13.0.tgz(r-4.5-any)
TOP_1.13.0.tar.gz(r-4.7-any)TOP_1.13.0.tar.gz(r-4.6-any)
TOP_1.13.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
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-1.13.0(bioc 3.24)TOP-1.12.0(bioc 3.23)

software survival geneexpression

4.82 score 66 scripts 14 exports 212 dependencies

Last updated from:391b4a30ad. Checks:7 NOTE, 2 OK, 1 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	269
linux-devel-x86_64	NOTE	398
source / vignettes	OK	385
linux-release-x86_64	NOTE	457
macos-release-arm64	FAIL	155
macos-oldrel-arm64	NOTE	170
windows-devel	NOTE	278
windows-release	NOTE	306
windows-oldrel	NOTE	313
wasm-release	OK	248

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 circlize class ClassifyR cli clock cluster codetools colorspace corrplot cowplot cpp11 crayon crosstalk curl data.table DBI dcanr DelayedArray Deriv diagram digest directPA doBy doParallel doRNG dplyr e1071 evaluate farver fastmap fontawesome foreach forecast foreign formatR Formula fracdiff fs futile.logger futile.options future future.apply genefilter generics GenomicRanges ggforce ggnewscale ggplot2 ggpubr ggraph ggrepel ggsci ggsignif ggthemes ggupset glmnet GlobalOptions 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 lmtest lubridate magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime minqa ModelMetrics modelr MultiAssayExperiment nlme nloptr nnet numDeriv openssl otel parallelly pbkrtest pillar pkgconfig plotly plyr png polyclip polynom pROC prodlim progressr promises proxy purrr quantreg R6 ranger rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack recipes reformulas reshape2 rlang rmarkdown rngtools rpart RSQLite rstatix rstudioapi S4Arrays S4Vectors S7 sass scales Seqinfo shape snow SparseArray SparseM sparsevctrs SQUAREM statmod stringi stringr SummarizedExperiment survival sys systemfonts tibble tidygraph tidyr tidyselect timechange timeDate tinytex tweenr tzdb urca utf8 vctrs viridis viridisLite withr xfun XML xtable XVector yaml zoo

Tranferable Omics Pediction

Rendered fromBuildingATOPModel.Rmdusingknitr::rmarkdown

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