Package: ivygapSE 1.27.0

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

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ivygapSE.pdf |ivygapSE.html✨
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-1.27.0(bioc 3.20)ivygapSE-1.26.0(bioc 3.19)

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

bioconductor-package

9 exports 0.82 score 148 dependencies

Last updated 2 months agofrom:7c114af8ba

Exports:designOverview exprByType getRefLimma ivyGlimpse makeGeneSets nomenclat subBlockDetails tumorDetails vocab

Dependencies:abind askpass backports base64enc Biobase BiocGenerics boot brio broom bslib cachem callr car carData cli colorspace commonmark corrplot cowplot cpp11 crayon crosstalk curl data.table DelayedArray desc diffobj digest dplyr evaluate exactRankTests fansi farver fastmap fontawesome fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggplot2 ggpubr ggrepel ggsci ggsignif ggtext glue gridExtra gridtext gtable highr htmltools htmlwidgets httpuv httr hwriter IRanges isoband jpeg jquerylib jsonlite km.ci KMsurv knitr labeling later lattice lazyeval lifecycle lme4 magrittr markdown MASS Matrix MatrixGenerics MatrixModels matrixStats maxstat memoise mgcv mime minqa munsell mvtnorm nlme nloptr nnet numDeriv openssl pbkrtest pillar pkgbuild pkgconfig pkgload plotly plyr png polynom praise processx promises ps purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen rematch2 rlang rmarkdown rprojroot rstatix S4Arrays S4Vectors sass scales shiny sourcetools SparseArray SparseM stringi stringr SummarizedExperiment survival survminer survMisc sys testthat tibble tidyr tidyselect tinytex UCSC.utils UpSetR utf8 vctrs viridisLite waldo withr xfun xml2 xtable XVector yaml zlibbioc zoo

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

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

Rendered fromivygapSE.Rmdusingknitr::rmarkdownon Jun 17 2024.

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)