Package: exploreSE 0.99.18

Jasper Spitzer

exploreSE: Explorer for Your Bulk RNA Seq Analyses

Interactive exploration of a Summarized experiment and associated DE analyses. A shiny app to inspect and interact with pre-calculated differential expression and functional enrichment results, and to facilitate comparisons between multiple models. This is meant to be a tool for exploration and discussion, rather than analysis.

Authors:Jasper Spitzer [aut, cre]

exploreSE_0.99.18.tar.gz
exploreSE_0.99.18.zip(r-4.7-any)exploreSE_0.99.18.zip(r-4.6-any)exploreSE_0.99.18.zip(r-4.5-any)
exploreSE_0.99.18.tgz(r-4.6-any)exploreSE_0.99.18.tgz(r-4.5-any)
exploreSE_0.99.18.tar.gz(r-4.7-any)exploreSE_0.99.18.tar.gz(r-4.6-any)
exploreSE_0.99.18.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
exploreSE/json (API)

# Install 'exploreSE' in R:

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

Bug tracker:https://github.com/jaspitzer/explorese/issues

Datasets:

baseline - DE results for airway - baseline
baseline_down_go - Example GO enrichments for the baseline model
baseline_up_go - Example GO enrichments for the baseline model
cell_controlled - DE results for airway - cell-controlled
controlled_down_go - Example GO enrichments for the cell_controlled model
controlled_up_go - Example GO enrichments for the cell controlled model
example_contexts - Example context lists

On BioConductor:exploreSE-0.99.17(bioc 3.24)

shinyapps rnaseq visualization geneexpression pathways go

4.95 score 1 stars 4 scripts 152 downloads 4 exports 175 dependencies

Last updated from:7c3b2e73b4. Checks:1 WARNING, 5 NOTE, 2 OK, 2 ERROR. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	202
linux-devel	NOTE	367
source / vignettes	OK	521
linux-release	NOTE	491
macos-release	NOTE	325
macos-oldrel	ERROR	152
windows-devel	NOTE	341
windows-release	NOTE	340
windows-oldrel	ERROR	242
wasm-release	OK	222

Exports:%>%exploreSE get.gos get.gsea

Dependencies:abind aisdk AnnotationDbi ape aplot askpass assertthat babelgene base64enc BH Biobase BiocBaseUtils BiocGenerics BiocParallel Biostrings bit bit64 blob bslib cachem callr cli clipr cluster clusterProfiler codetools colourpicker commonmark cpp11 crayon crosstalk curl data.table DBI DeeDeeExperiment DelayedArray DESeq2 digest DOSE dplyr DT edgeR enrichit enrichplot evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver forcats formatR fs futile.logger futile.options gdtools generics GenomicRanges ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree glue GO.db GOSemSim gridGraphics gson gtable highr hms htmltools htmlwidgets httpuv httr httr2 igraph IRanges isoband jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mime miniUI msigdbr nlme openssl org.Hs.eg.db org.Mm.eg.db otel patchwork pillar pkgconfig plotly plyr png polyclip prettyunits processx progress promises ps purrr qvalue R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen readr reshape2 rlang rmarkdown RSQLite S4Arrays S4Vectors S7 sass scales scatterpie Seqinfo shiny shinyjs shinyWidgets SingleCellExperiment snow sourcetools SparseArray statmod stringi stringr SummarizedExperiment sys systemfonts tibble tidydr tidyr tidyselect tidytree tinytex treeio tweenr tzdb utf8 vctrs viridisLite vroom withr writexl xfun xtable XVector yaml yulab.utils

Introduction to exploreSE

Rendered fromIntroduction.Rmdusingknitr::rmarkdown

Last update: 2026-10-29
Started: 2026-07-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
DE results for airway - baseline	baseline
Example GO enrichments for the baseline model	baseline_down_go
Example GO enrichments for the baseline model	baseline_up_go
DE results for airway - cell-controlled	cell_controlled
Example GO enrichments for the cell_controlled model	controlled_down_go
Example GO enrichments for the cell controlled model	controlled_up_go
Example context lists	example_contexts
exploreSE	exploreSE
Calculate GO Enrichments for a given comparison	get.gos
Calculate GSEA Enrichments for a given comparison	get.gsea