Package: categoryCompare 1.51.0

Robert M. Flight

categoryCompare: Meta-analysis of high-throughput experiments using feature annotations

Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).

Authors:Robert M. Flight <[email protected]>

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categoryCompare/json (API)
NEWS

# Install 'categoryCompare' in R:

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

Bug tracker:https://github.com/rmflight/categorycompare/issues

Datasets:

ccOpts - Test data for 'categoryCompare'
ccResults - Test data for 'categoryCompare'
ccResultsBPHier - Test data for 'categoryCompare'
enrichLists - Test data for 'categoryCompare'
gUniverse - Test data for 'categoryCompare'
geneLists - Test data for 'categoryCompare'
gseaRes - Test data for 'categoryCompare'
table10 - Test data for 'categoryCompare'
table48 - Test data for 'categoryCompare'

On BioConductor:categoryCompare-1.51.0(bioc 3.21)categoryCompare-1.50.0(bioc 3.20)

annotation go multiplecomparison pathways geneexpression bioconductor

6.68 score 6 stars 252 downloads 12 mentions 38 exports 84 dependencies

Last updated 2 months agofrom:570b4b8bb8. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	NOTE	Nov 29 2024
R-4.5-linux	NOTE	Nov 29 2024
R-4.4-win	NOTE	Nov 29 2024
R-4.4-mac	NOTE	Nov 29 2024
R-4.3-win	NOTE	Nov 29 2024
R-4.3-mac	NOTE	Nov 29 2024

Exports:allAnnotation annotation breakEdges ccCompare ccEnrich ccOutCyt ccType ccType<-compareColors compareColors<-compareIndx compareNames compareNames<-cwReload cytOutData cytOutNodes fdr fdr<-fdrvalues geneAnnMapping graphType graphType<-hyperGTestCC listNames mainGraph mainTable mergeLists minCount minCount<-ontology outType outType<-pvalueCutoff pvalueCutoff<-pvalueType pvalueType<-resetColors sigID

Dependencies:annotate AnnotationDbi AnnotationForge askpass backports base64enc base64url BH Biobase BiocGenerics Biostrings bit bit64 bitops blob cachem Category caTools cli colorspace cpp11 crayon curl DBI digest evaluate fansi fastmap fs genefilter generics GenomeInfoDb GenomeInfoDbData glue GO.db GOstats gplots graph GSEABase gtools htmltools httr hwriter IRanges IRdisplay IRkernel jsonlite KEGGREST KernSmooth lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pbdZMQ pillar pkgconfig plogr png R6 RBGL RColorBrewer RCurl RCy3 repr Rgraphviz RJSONIO rlang RSQLite S4Vectors stringi survival sys UCSC.utils utf8 uuid vctrs XML xtable XVector zlibbioc

categoryCompare: High-throughput data meta-analysis using gene annotations

Rendered fromcategoryCompare_vignette.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2021-06-17
Started: 2014-08-13

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Meta-analysis of high-throughput experiments using feature annotations	categoryCompare-package categoryCompare
Methods for Function 'breakEdges' in Package 'categoryCompare'	breakEdges breakEdges,ccCompareResult,numeric-method breakEdges,numeric,numeric-method breakEdges-methods
Comparison of enriched annotations	ccCompare ccCompare,ccEnrichCollection,ccOptions-method ccCompare,GENccEnrichResult,ccOptions-method ccCompare,GOccEnrichResult,ccOptions-method ccCompare,KEGGccEnrichResult,ccOptions-method ccCompare-methods
Class '"ccCompareCollection"'	ccCompareCollection ccCompareCollection-class
Methods for Function 'ccCompareGeneric' in Package 'categoryCompare'	ccCompareGeneric ccCompareGeneric-methods ccOptions,ccCompareGeneric-method GENccEnrichResult,ccCompareGeneric-method
Class '"ccCompareResult"'	allAnnotation allAnnotation,ccCompareResult-method ccCompareResult ccCompareResult-class mainGraph mainGraph,ccCompareResult-method mainTable mainTable,ccCompareResult-method
Test data for 'categoryCompare'	ccData ccOpts ccResults ccResultsBPHier enrichLists geneLists gseaRes gUniverse table10 table48
Perform annotation enrichment for multiple gene lists	ccEnrich ccEnrich,ccGeneList-method ccEnrich-method
Class "ccEnrichCollection"	ccEnrichCollection ccEnrichCollection-class graphType,ccEnrichCollection-method graphType<-,ccEnrichCollection-method minCount<-,ccEnrichCollection-method pvalueCutoff<-,ccEnrichCollection-method pvalueType<-,ccEnrichCollection-method
Class "ccEnrichResult"	ccEnrichResult ccEnrichResult-class fdr,ccEnrichResult-method GOccEnrichResult GOccEnrichResult-class graphType,ccEnrichResult-method graphType<-,ccEnrichResult-method KEGGccEnrichResult KEGGccEnrichResult-class minCount,ccEnrichResult-method minCount<-,ccEnrichResult-method pvalueCutoff,ccEnrichResult-method pvalueCutoff<-,ccEnrichResult-method pvalueType,ccEnrichResult-method pvalueType<-,ccEnrichResult-method [,ccEnrichResult,ANY,ANY,ANY-method [,ccEnrichResult,ANY,ANY-method
Class "ccGeneList"	ccGeneList ccGeneList-class ccType ccType,ccGeneList-method ccType<- ccType<-,ccGeneList-method fdr,ccGeneList-method fdr<-,ccGeneList-method listNames,ccGeneList-method pvalueCutoff,ccGeneList-method pvalueCutoff<-,ccGeneList-method testDirection,ccGeneList-method
Class "ccOptions"	ccOptions ccOptions-class compareColors compareColors,ccOptions-method compareColors<- compareColors<-,ccOptions-method compareIndx compareIndx,ccOptions-method compareNames compareNames,ccOptions-method compareNames<- compareNames<-,ccOptions-method cssClass cssClass,ccOptions-method listNames,ccOptions-method listNames<-,ccOptions-method outType outType,ccOptions-method outType<- outType<-,ccOptions-method
Methods for Function 'ccOutCyt' in Package 'categoryCompare'	ccOutCyt ccOutCyt,ccCompareResult,ccOptions-method ccOutCyt-methods
Class '"ccSigList"'	annotation,ccSigList-method category,ccSigList-method ccSigList ccSigList-class ontology,ccSigList-method sigID,ccSigList-method
Methods for Function 'cwReload' in Package 'categoryCompare'	cwReload cwReload,numeric,ccOptions-method cwReload,numeric,character,ccOptions-method cwReload-methods
Methods for Function 'cytOutData'	cytOutData cytOutData,list,ccCompareResult,mergedData-method cytOutData,list,ccCompareResult,missing-method cytOutData,list,missing,missing-method cytOutData-methods
Methods for Function 'cytOutNodes'	cytOutNodes cytOutNodes,character,numeric,list-method cytOutNodes,character,numeric,missing-method cytOutNodes-methods
Number of FDR runs to perform	fdr fdr<-
Class '"GENccEnrichResult"'	category,GENccEnrichResult-method ccCompareGeneric,GENccEnrichResult,ccOptions-method GENccEnrichResult GENccEnrichResult-class geneAnnMapping geneAnnMapping,GENccEnrichResult-method graphType,GENccEnrichResult-method graphType<-,GENccEnrichResult-method ontology,GENccEnrichResult-method sigID [,GENccEnrichResult,ANY,ANY,ANY-method [,GENccEnrichResult,ANY,ANY-method
Entrez to name, symbol, GO and path conversion, as well as general ID to ID conversion.	getAnnotation getGeneName getGeneSymbol getGO2ALLEGS getPATH2EG
graphType	graphType graphType-methods graphType<-
Class "HyperGParamsCC"	fdr,HyperGParamsCC-method fdr<-,HyperGParamsCC-method GOHyperGParams GOHyperGParams-class GOHyperGParamsCC GOHyperGParamsCC-class HyperGParamsCC HyperGParamsCC-class KEGGHyperGParams KEGGHyperGParams-class KEGGHyperGParamsCC KEGGHyperGParamsCC-class
Class "HyperGResultCC"	fdr,HyperGResultCC-method fdrvalues fdrvalues,HyperGResultCC-method fdrvalues-method GOHyperGResultCC GOHyperGResultCC-class HyperGResultCC HyperGResultCC-class KEGGHyperGResultCC KEGGHyperGResultCC-class minCount,HyperGResultCC-method minCount<-,HyperGResultCC-method pCC,HyperGResultCC-method pvalueCutoff<-,HyperGResultCC-method pvalueType,HyperGResultCC-method pvalueType<-,HyperGResultCC-method
Hypergeometric testing with false discovery rate	hyperGTestCC hyperGTestCC,HyperGParamsCC hyperGTestCC,HyperGParamsCC-method
listNames	listNames
Class '"mergedData"'	mergedData-class
Function 'mergeLists' in Package 'categoryCompare'	mergeLists mergeLists,ccGeneList,ccOptions-method mergeLists-methods
minCount	minCount minCount<-
Delete nodes with less than a certain number of genes annotated	minNodes minNodes,CytoscapeWindowClass,numeric-method
Type of p-values to return from object	pvalueType pvalueType<-
resetColors	resetColors resetColors,numeric,ccOptions-method resetColors-methods
Methods for Function show in Package `categoryCompare'	show,HyperGResultCC-method show-methods summary,HyperGResultCC-method summary-methods