Package: sparrow 1.13.1

Steve Lianoglou

sparrow: Take command of set enrichment analyses through a unified interface

Provides a unified interface to a variety of GSEA techniques from different bioconductor packages. Results are harmonized into a single object and can be interrogated uniformly for quick exploration and interpretation of results. Interactive exploration of GSEA results is enabled through a shiny app provided by a sparrow.shiny sibling package.

Authors:Steve Lianoglou [aut, cre], Arkadiusz Gladki [ctb], Aratus Informatics, LLC [fnd], Denali Therapeutics [fnd], Genentech [fnd]

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NEWS

# Install 'sparrow' in R:

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

Bug tracker:https://github.com/lianos/sparrow/issues

On BioConductor:sparrow-1.13.0(bioc 3.21)sparrow-1.12.0(bioc 3.20)

genesetenrichment pathways bioinformatics gsea

6.97 score 20 stars 1 packages 13 scripts 294 downloads 74 exports 136 dependencies

Last updated 8 days agofrom:f774c1797b. Checks:OK: 1 WARNING: 1 ERROR: 5. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 15 2024
R-4.5-win	ERROR	Nov 15 2024
R-4.5-linux	WARNING	Nov 15 2024
R-4.4-win	ERROR	Nov 15 2024
R-4.4-mac	ERROR	Nov 15 2024
R-4.3-win	ERROR	Nov 15 2024
R-4.3-mac	ERROR	Nov 15 2024

Exports:addCollectionMetadata addGeneSetMetadata annotateGeneSetMembership calculateIndividualLogFC collectionMetadata combine conform convertIdentifiers corplot eigenWeightedMean encode_gskey exampleBiocSet exampleDgeResult exampleExpressionSet exampleGeneSetDb exampleGeneSetDF exampleGeneSets exampleSparrowResult failWith featureIdMap featureIds featureIdType featureIdType<-geneSet geneSetCollectionURLfunction geneSetCollectionURLfunction<-geneSetDb GeneSetDb geneSets geneSetsStats geneSetSummaryByGenes geneSetURL getKeggCollection getKeggGeneSetDb getMSigCollection getMSigGeneSetDb getPantherCollection getPantherGeneSetDb getReactomeCollection goseq gsdScore hasGeneSet hasGeneSetCollection incidenceMatrix iplot is.active is.conformed logFC mgheatmap mgheatmap2 msg nrow ora p.matrix plot_ora_bias randomGeneSetDb renameCollections renameRows result resultNames results scale_rows scoreSingleSamples seas sparrow_methods species_info split_gskey subsetByFeatures tabulateResults unconform validateInputs volcanoPlot volcanoStatsTable zScore

Dependencies:abind annotate AnnotationDbi askpass babelgene backports base64enc BH Biobase BiocGenerics BiocIO BiocParallel BiocSet Biostrings bit bit64 blob bslib cachem checkmate circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon crosstalk curl data.table DBI DelayedArray DelayedMatrixStats digest doParallel dplyr edgeR evaluate fansi farver fastmap fontawesome foreach formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GetoptLong ggplot2 GlobalOptions glue graph gridExtra GSEABase gtable highr htmltools htmlwidgets httr IRanges irlba isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme ontologyIndex openssl pillar pkgconfig plogr plotly plyr png promises purrr R6 rappdirs RColorBrewer Rcpp rjson rlang rmarkdown RSQLite S4Arrays S4Vectors sass scales shape snow SparseArray sparseMatrixStats statmod stringi stringr sys tibble tidyr tidyselect tinytex UCSC.utils utf8 vctrs viridis viridisLite withr xfun XML xtable XVector yaml zlibbioc

Performing gene set enrichment analyses with sparrow

Steve Lianoglou

Rendered fromsparrow.Rmdusingknitr::rmarkdownon Nov 15 2024.

Last update: 2021-10-13
Started: 2021-05-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Subset whole genesets from a GeneSetDb	[,GeneSetDb,ANY,ANY,ANY-method
Add metadata at the geneset level.	addGeneSetMetadata
Checks equality (feature parity) between GeneSetDb objects	all.equal.GeneSetDb
Annotates rows of a data.frame with geneset membership from a GeneSetDb	annotateGeneSetMembership
Utility function to run limma differential expression analysis	calculateIndividualLogFC
Gene Set Collection Metadata	addCollectionMetadata collectionMetadata collectionMetadata,GeneSetDb,character,character-method collectionMetadata,GeneSetDb,character,missing-method collectionMetadata,GeneSetDb,missing,missing-method featureIdType featureIdType,GeneSetDb-method featureIdType<- featureIdType<-,GeneSetDb-method geneSetURL geneSetURL,GeneSetDb-method geneSetURL,SparrowResult-method
Combines two GeneSetDb objects together	combine,GeneSetDb,GeneSetDb-method
Combines two SparrowResult objects together.	combine,SparrowResult,SparrowResult-method
(Re)-map geneset IDs to the rows in an expression object.	conform conform,GeneSetDb-method is.conformed unconform unconform,GeneSetDb-method
Convert a GeneSetDb to other formats.	as.data.frame as.data.frame.GeneSetDb as.data.table as.data.table.GeneSetDb as.list conversion
Converts internal feature identifiers in a GeneSetDb to a set of new ones.	convertIdentifiers convertIdentifiers,BiocSet-method convertIdentifiers,GeneSetDb-method
Plots the correlation among the columns of a numeric matrix.	corplot
Single sample gene set score by a weighted average of the genes in geneset	eigenWeightedMean
Converts collection,name combination to key for geneset	encode_gskey split_gskey
Functions that load data for use in examples and testing.	exampleBiocSet exampleDgeResult exampleExpressionSet exampleGeneSetDb exampleGeneSetDF exampleGeneSets exampleSparrowResult
Utility function to try and fail with grace.	failWith
Fetch the featureIdMap for a 'GeneSetDb'	featureIdMap featureIdMap,GeneSetDb-method
Returns the relevant featureIds for a given geneset.	featureIds featureIds,GeneSetDb-method featureIds,SparrowResult-method
Fetches information for a gene set	geneSet geneSet,GeneSetDb-method geneSet,SparrowResult-method
Get/set the gene set collection url function for a geneset collection	geneSetCollectionURLfunction geneSetCollectionURLfunction,GeneSetDb-method geneSetCollectionURLfunction,SparrowResult-method geneSetCollectionURLfunction<- geneSetCollectionURLfunction<-,GeneSetDb-method
Fetches the GeneSetDb from SparrowResult	geneSetDb
A container for geneset definitions.	.GeneSetDb GeneSetDb GeneSetDb-class
Fetch the active (or all) gene sets from a GeneSetDb or SparrowResult	geneSets geneSets,GeneSetDb-method geneSets,SparrowResult-method length,GeneSetDb-method nrow,GeneSetDb-method
Summarizes useful statistics per gene set from a SparrowResult	geneSetsStats
Summarize geneset:feature relationships for specified set of features	geneSetSummaryByGenes geneSetSummaryByGenes,GeneSetDb-method geneSetSummaryByGenes,SparrowResult-method
Retrieves the KEGG gene set collection via its REST API	getKeggCollection getKeggGeneSetDb
Fetches gene set collections from the moleular signature database (MSigDB)	getMSigCollection getMSigGeneSetDb
Get pathways/GOslim collections from PANTHER.db Biocondcutor package.	getPantherCollection getPantherGeneSetDb
Retrieve gene set collections from from reactome.db	getReactomeCollection getReactomeGeneSetDb
Perform goseq Enrichment tests across a GeneSetDb.	goseq
Single sample geneset score using SVD based eigengene value per sample.	gsdScore
Check to see if the GeneSetDb has a collection,name GeneSet defined	hasGeneSet
Check if a collection exists in the 'GeneSetDb'	hasGeneSetCollection
Creates a 1/0 matrix to indicate geneset membership to target object.	incidenceMatrix
Visualize gene level behavior of genes within a geneset across a contrast.	iplot
Interrogate "active" status of a given geneset.	is.active
Extract the individual fold changes statistics for elements in the expression object.	logFC
Creates a "geneset smart" ComplexHeatmap::Heatmap	mgheatmap
Creates a "geneset smart" ComplexHeatmap::Heatmap	mgheatmap2
Utility function to cat a message to stderr (by default)	msg
Performs an overrepresentation analysis, (optionally) accounting for bias.	ora plot_ora_bias
Assembles a matrix of nominal or adjusted pvalues from a sparrow::seas result	p.matrix
Generates a fake GeneSetDb by sampling from features in a seas input.	randomGeneSetDb
Rename the collections in a GeneSetDb	renameCollections
Smartly/easily rename the rows of an object.	renameRows
Interrogate the results of a sparrow::seas analysis stored in a SparrowResult	result result.SparrowResult resultNames results tabulateResults
Centers and scales the rows of a numeric matrix.	scale_rows
Generates single sample gene set scores across a datasets by many methods	scoreSingleSamples
Performs a plethora of set enrichment analyses over varied inputs.	seas
Lists the supported GSEA methods by sparrow	sparrow_methods
A SparrowResult object holds the results from a sparrow::seas() call.	.SparrowResult SparrowResult SparrowResult-class
Match a species query to the regularized species info.	species_info
Normalize a vector of ssGSEA scores in the ssGSEA way.	ssGSEA.normalize
Subset GeneSetDb to only include specified genesets.	subset.GeneSetDb
Subset a GeneSetDb to only include geneSets with specified features.	subsetByFeatures subsetByFeatures,GeneSetDb-method
Validate the input objects to a GSEA call.	validateInputs
Create an interactive volcano plot	volcanoPlot
Extracts x and y axis values from objects to create input for volcano plot	volcanoStatsTable
Calculate single sample geneset score by average z-score method	zScore