Package: ivygapSE 1.34.0

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_1.34.0.tar.gz
ivygapSE_1.34.0.zip(r-4.7)ivygapSE_1.34.0.zip(r-4.6)ivygapSE_1.34.0.zip(r-4.5)
ivygapSE_1.34.0.tgz(r-4.6-any)ivygapSE_1.34.0.tgz(r-4.5-any)
ivygapSE_1.34.0.tar.gz(r-4.7-any)ivygapSE_1.34.0.tar.gz(r-4.6-any)
ivygapSE_1.34.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
ivygapSE/json (API)

# Install 'ivygapSE' in R:

install.packages('ivygapSE', repos = c('https://bioc-release.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

4.20 score 16 scripts 417 downloads 9 exports 143 dependencies

Last updated from:edba63d6fb (on RELEASE_3_23). Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: no.

Target	Result	Time	Files	Syslog
bioc-checks	ERROR	194
linux-devel-x86_64	NOTE	382
source / vignettes	OK	332
linux-release-x86_64	NOTE	322
macos-release-arm64	NOTE	192
macos-oldrel-arm64	NOTE	175
windows-devel	NOTE	269
windows-release	NOTE	238
windows-oldrel	NOTE	227
wasm-release	OK	172

Exports:designOverview exprByType getRefLimma ivyGlimpse makeGeneSets nomenclat subBlockDetails tumorDetails vocab

Dependencies:abind askpass backports base64enc Biobase BiocGenerics boot broom bslib cachem car carData cli colorspace commonmark corrplot cowplot cpp11 crosstalk curl data.table DelayedArray Deriv digest doBy dplyr evaluate exactRankTests farver fastmap fontawesome forecast Formula fracdiff fs generics GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif ggtext glue gridExtra gridtext gtable highr htmltools htmlwidgets httpuv httr hwriter IRanges isoband jpeg jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle litedown lme4 lmtest magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats maxstat memoise mgcv microbenchmark mime minqa modelr mvtnorm nlme nloptr nnet numDeriv openssl otel pbkrtest pillar pkgconfig plotly plyr png polynom promises purrr quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack reformulas rlang rmarkdown rstatix S4Arrays S4Vectors S7 sass scales Seqinfo shiny sourcetools SparseArray SparseM stringi stringr SummarizedExperiment survival survminer sys tibble tidyr tidyselect timeDate tinytex UpSetR urca utf8 vctrs viridisLite withr xfun xml2 xtable XVector yaml zoo

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

Vincent J. Carey, stvjc at channing.harvard.edu

Rendered fromivygapSE.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2018-04-16
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)