Package: GOstats 2.71.0

Bioconductor Package Maintainer

GOstats: Tools for manipulating GO and microarrays

A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.

Authors:Robert Gentleman [aut], Seth Falcon [ctb], Robert Castelo [ctb], Sonali Kumari [ctb], Dennis Ndubi [ctb], Bioconductor Package Maintainer [cre]

GOstats_2.71.0.tar.gz
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GOstats.pdf |GOstats.html✨
GOstats/json (API)

# Install 'GOstats' in R:

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

Datasets:

Bdists - Distance matrices for the BCR/ABL and NEG subgroups.
Ndists - Distance matrices for the BCR/ABL and NEG subgroups.

On BioConductor:GOstats-2.71.0(bioc 3.20)GOstats-2.70.0(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

35 exports 3.06 score 57 dependencies 14 dependents 368 mentions

Last updated 2 months agofrom:f8c38a14f9

Exports:annotation compCorrGraph compGdist description enumPairs expectedCounts geneCounts geneIds geneIdUniverse geneMappedCount goDag GOGraph htmlReport hyperGTest idx2dimnames inducedTermGraph isTriad makeGOGraph notConn oddsRatios oneGOGraph plotGOTermGraph probeSetSummary pvalues reduce2Degreek shortestPath simLL simLP simUI summary termGraphs testName triadCensus universeCounts universeMappedCount

Dependencies:annotate AnnotationDbi AnnotationForge askpass BH Biobase BiocGenerics Biostrings bit bit64 bitops blob cachem Category cli cpp11 crayon curl DBI fastmap genefilter GenomeInfoDb GenomeInfoDbData glue GO.db graph GSEABase httr IRanges jsonlite KEGGREST lattice lifecycle Matrix MatrixGenerics matrixStats memoise mime openssl pkgconfig plogr png R6 RBGL RCurl Rgraphviz rlang RSQLite S4Vectors survival sys UCSC.utils vctrs XML xtable XVector zlibbioc

How To Use GOstats and Category to do Hypergeometric testing with unsupported model organisms

M. Carlson, Sonali Kumari

Rendered fromGOstatsForUnsupportedOrganisms.Rmdusingknitr::rmarkdownon Jun 22 2024.

Last update: 2023-06-05
Started: 2023-06-05

How To Use GOstats Testing Gene Lists for GO Term Association

S. Falcon, R. Gentleman, Dennis Ndubi

Rendered fromGOstatsHyperG.Rmdusingknitr::rmarkdownon Jun 22 2024.

Last update: 2023-04-10
Started: 2023-04-06

Visualizing and Distances Using GO

R. Gentleman, Sonali Kumari

Rendered fromGOvis.Rmdusingknitr::rmarkdownon Jun 22 2024.

Last update: 2023-04-04
Started: 2023-04-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Tools for manipulating GO and microarrays.	GOstats-package GOstats
A function to compute a correlation based graph from Gene Expression Data	compCorrGraph
A function to compute the distance between pairs of nodes in a graph.	compGdist
Class "GOHyperGResult"	conditional,GOHyperGResult-method expectedCounts,GOHyperGResult-method geneCounts,GOHyperGResult-method geneIdUniverse,GOHyperGResult-method goDag goDag,GOHyperGResult-method GOHyperGResult-class htmlReport,GOHyperGResult-method oddsRatios,GOHyperGResult-method pvalues,GOHyperGResult-method summary,GOHyperGResult-method
Defunct Functions in GOstats Package	combGOGraph getGoGraph GOHyperG GOKEGGHyperG GOLeaves GOstats-defunct hyperG2Affy hyperGtable selectedGenes
Hypergeometric Tests for GO term association	hyperGTest hyperGTest,GOHyperGParams-method hyperGTest,OBOHyperGParams-method
Index to Dimnames	idx2dimnames
Construct a GO Graph	makeGOGraph
Distance matrices for the BCR/ABL and NEG subgroups.	Bdists Ndists
Find genes that are not connected to the others.	notConn
Class "OBOHyperGResult"	conditional,OBOHyperGResult-method expectedCounts,OBOHyperGResult-method geneCounts,OBOHyperGResult-method geneIdUniverse,OBOHyperGResult-method goDag,OBOHyperGResult-method htmlReport,OBOHyperGResult-method OBOHyperGResult-class oddsRatios,OBOHyperGResult-method pvalues,OBOHyperGResult-method summary,OBOHyperGResult-method
Construct the GO graph given a set of leaves.	GOGraph oneGOGraph
Summarize Probe Sets Associated with a hyperGTest Result	probeSetSummary
Shortest Path Analysis	shortestPath
Functions to compute similarities between GO graphs and also between Entrez Gene IDs based on their induced GO graphs.	simLL simLP simUI
Extraction and Plotting of GO Terms from a GOHyperGResult Object	inducedTermGraph plotGOTermGraph termGraphs
Triad Functions	enumPairs isTriad reduce2Degreek triad triadCensus