Package: ivygapSE 1.29.0

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_1.29.0.tar.gz
ivygapSE_1.29.0.zip(r-4.5)ivygapSE_1.29.0.zip(r-4.4)ivygapSE_1.29.0.zip(r-4.3)
ivygapSE_1.29.0.tgz(r-4.4-any)ivygapSE_1.29.0.tgz(r-4.3-any)
ivygapSE_1.29.0.tar.gz(r-4.5-noble)ivygapSE_1.29.0.tar.gz(r-4.4-noble)
ivygapSE_1.29.0.tgz(r-4.4-emscripten)ivygapSE_1.29.0.tgz(r-4.3-emscripten)
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.

transcription software visualization survival geneexpression sequencing

4.20 score 16 scripts 190 downloads 9 exports 140 dependencies

Last updated 23 days agofrom:4df1812cd6. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	NOTE	Oct 31 2024
R-4.3-mac	NOTE	Oct 31 2024

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 crayon crosstalk curl data.table DelayedArray Deriv digest doBy dplyr evaluate exactRankTests fansi farver fastmap fontawesome Formula 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 microbenchmark mime minqa modelr munsell mvtnorm nlme nloptr nnet numDeriv openssl pbkrtest pillar pkgconfig plotly plyr png polynom promises purrr quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen rlang rmarkdown rstatix S4Arrays S4Vectors sass scales shiny sourcetools SparseArray SparseM stringi stringr SummarizedExperiment survival survminer survMisc sys tibble tidyr tidyselect tinytex UCSC.utils UpSetR utf8 vctrs viridisLite 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 Oct 30 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)