Package: ivygapSE 1.35.2

VJ Carey

ivygapSE: A SummarizedExperiment for Ivy-GAP data

Define a SummarizedExperiment and exploratory app for Ivy-GAP glioblastoma image, expression, and clinical data.

Authors:Vince Carey

ivygapSE_1.35.2.tar.gz
ivygapSE_1.35.2.zip(r-4.7)ivygapSE_1.35.2.zip(r-4.6)ivygapSE_1.35.2.zip(r-4.5)
ivygapSE_1.35.2.tgz(r-4.6-any)ivygapSE_1.35.2.tgz(r-4.5-any)
ivygapSE_1.35.2.tar.gz(r-4.7-any)ivygapSE_1.35.2.tar.gz(r-4.6-any)
ivygapSE_1.35.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ivygapSE/json (API)

# Install 'ivygapSE' in R:

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

Datasets:

ivySE - IvySE: SummarizedExperiment for IvyGAP expression data and metadata

On BioConductor:ivygapSE-1.35.0(bioc 3.24)ivygapSE-1.34.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

transcription software visualization survival geneexpression sequencing

4.43 score 18 scripts 9 exports 96 dependencies

Last updated from:e705549d5f. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
bioc-checks	ERROR	196
linux-devel-x86_64	NOTE	372
source / vignettes	OK	313
linux-release-x86_64	NOTE	317
macos-release-arm64	NOTE	205
macos-oldrel-arm64	NOTE	197
windows-devel	NOTE	259
windows-release	NOTE	233
windows-oldrel	NOTE	231
wasm-release	OK	139

Exports:designOverview exprByType getRefLimma ivyGlimpse makeGeneSets nomenclat subBlockDetails tumorDetails vocab

Dependencies:abind askpass base64enc Biobase BiocFileCache BiocGenerics bit bit64 blob bslib cachem cli commonmark cpp11 crosstalk curl data.table DBI dbplyr DelayedArray digest dplyr evaluate farver fastmap filelock fontawesome fs generics GenomicRanges ggplot2 glue gtable highr htmltools htmlwidgets httpuv httr httr2 hwriter IRanges isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl otel pillar pkgconfig plotly promises purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown RSQLite S4Arrays S4Vectors S7 sass scales Seqinfo shiny sourcetools SparseArray stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun xtable XVector yaml

ivygapSE -- Bioconductor container for Ivy-GAP expression and metadata

Introduction | Background on the ivyGlimpse app | Summary information on the underlying data | Additional details | Basic experimental design layout | Tumor-level details | Sub-block-level details | Details on RNA-seq samples | Key RNA-seq subsets | Subsets of design origin | Subsets based on structure | A simple differential expression study | Differential expression by molecular subtype | Classification of structural character | Next steps

Rendered fromivygapSE.Rmdusingknitr::rmarkdown

Last update: 2026-06-22
Started: 2017-06-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
render design overview	designOverview nomenclat
simple plot of expression values by structure/expression-based selection in IvyGAP	exprByType
provide access to a limma analysis of RNA-seq profiles for reference histology samples	getRefLimma
simple app to explore image property quantifications in relation to survival and expression	ivyGlimpse
ivySE: SummarizedExperiment for IvyGAP expression data and metadata	ivySE
demonstration of gene set construction for ivyGlimpse app	makeGeneSets
helper functions for data access	subBlockDetails tumorDetails vocab

Usage by other packages (reverse dependencies)