Package: simplifyEnrichment 2.7.0

Zuguang Gu

simplifyEnrichment: Simplify Functional Enrichment Results

A new clustering algorithm, "binary cut", for clustering similarity matrices of functional terms is implemeted in this package. It also provides functions for visualizing, summarizing and comparing the clusterings.

Authors:Zuguang Gu [aut, cre]

simplifyEnrichment_2.7.0.tar.gz
simplifyEnrichment_2.7.0.zip(r-4.7)simplifyEnrichment_2.7.0.zip(r-4.6)simplifyEnrichment_2.7.0.zip(r-4.5)
simplifyEnrichment_2.7.0.tgz(r-4.6-any)simplifyEnrichment_2.7.0.tgz(r-4.5-any)
simplifyEnrichment_2.7.0.tar.gz(r-4.7-any)simplifyEnrichment_2.7.0.tar.gz(r-4.6-any)
simplifyEnrichment_2.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
simplifyEnrichment/json (API)

# Install 'simplifyEnrichment' in R:

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

Bug tracker:https://github.com/jokergoo/simplifyenrichment/issues

On BioConductor:simplifyEnrichment-2.7.0(bioc 3.24)simplifyEnrichment-2.6.0(bioc 3.23)

software visualization go clustering genesetenrichment

8.24 score 126 stars 308 scripts 1 mentions 44 exports 83 dependencies

Last updated from:a14432cbeb. Checks:1 ERROR, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	236
linux-devel-x86_64	OK	328
source / vignettes	OK	288
linux-release-x86_64	OK	328
macos-release-arm64	OK	153
macos-oldrel-arm64	OK	206
windows-devel	OK	223
windows-release	OK	226
windows-oldrel	OK	247
wasm-release	OK	236

Exports:all_clustering_methods anno_word_cloud anno_word_cloud_from_GO binary_cut cluster_by_apcluster cluster_by_dynamicTreeCut cluster_by_fast_greedy cluster_by_hdbscan cluster_by_kmeans cluster_by_leading_eigen cluster_by_louvain cluster_by_MCL cluster_by_mclust cluster_by_pam cluster_by_walktrap cluster_terms cmp_make_clusters cmp_make_plot compare_clustering_methods count_words dend_node_apply difference_score export_to_shiny_app GO_similarity guess_ont ht_clusters keyword_enrichment_from_GO partition_by_hclust partition_by_kmeans partition_by_kmeanspp partition_by_pam plot_binary_cut random_GO register_clustering_methods remove_clustering_methods reset_clustering_methods scale_fontsize se_opt select_cutoff simplifyEnrichment simplifyGO simplifyGOFromMultipleLists summarizeGO word_cloud_grob

Dependencies:AnnotationDbi askpass base64enc BH Biobase BiocGenerics Biostrings bit bit64 blob bslib cachem circlize cli clue cluster codetools colorspace commonmark ComplexHeatmap cpp11 crayon curl DBI digest doParallel fastmap fastmatch fontawesome foreach fs generics GetoptLong GlobalOptions glue GO.db htmltools httpuv httr igraph IRanges iterators jquerylib jsonlite KEGGREST later lattice lifecycle magrittr Matrix matrixStats memoise mime NLP openssl otel pkgconfig png Polychrome promises R6 rappdirs RColorBrewer Rcpp rjson rlang RSQLite S4Vectors sass scatterplot3d Seqinfo shape shiny simona slam sourcetools sys tm vctrs withr xml2 xtable XVector

The simplifyEnrichment package

Rendered fromsimplifyEnrichment.Rmdusingknitr::rmarkdown

Last update: 2024-09-13
Started: 2020-08-08

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Word cloud annotations	anno_word_cloud
Word cloud annotations from GO	anno_word_cloud_from_GO
Area above the eCDF curve	area_above_ecdf
Cluster terms based on their similarity matrix	cluster_by_apcluster cluster_by_dynamicTreeCut cluster_by_fast_greedy cluster_by_hdbscan cluster_by_kmeans cluster_by_leading_eigen cluster_by_louvain cluster_by_MCL cluster_by_mclust cluster_by_pam cluster_by_walktrap cluster_terms
Compare clustering methods	cmp_make_clusters cmp_make_plot compare_clustering_methods
Calculate word frequency	count_words
Apply functions on every node in a dendrogram	dend_node_apply edit_node
Difference score	difference_score
Interactively visualize the similarity heatmap	export_to_shiny_app
Calculate Gene Ontology (GO) semantic similarity matrix	GO_similarity guess_ont random_GO
Visualize the similarity matrix and the clustering	ht_clusters
Keyword enrichment for GO terms	keyword_enrichment_from_GO
Partition the matrix	partition_by_hclust partition_by_kmeans partition_by_kmeanspp partition_by_pam
Cluster functional terms by recursively binary cutting the similarity matrix	binary_cut plot_binary_cut
Configure clustering methods	all_clustering_methods register_clustering_methods remove_clustering_methods reset_clustering_methods
Scale font size	scale_fontsize
Global parameters	se_opt
Select the cutoff for binary cut	select_cutoff
Simplify Gene Ontology (GO) enrichment results	simplifyEnrichment simplifyGO
Perform simplifyGO analysis with multiple lists of GO IDs	simplifyGOFromMultipleLists
A simplified way to visualize enrichment in GO clusters	summarizeGO
A simple grob for the word cloud	heightDetails.word_cloud widthDetails.word_cloud word_cloud_grob