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adds taxonomy ids to species_info outputs

Feb 18, 2025

a51778d · Feb 18, 2025

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Name		Name	Last commit message	Last commit date
parent directory ..
figures		figures	More work to bring BiocSet use front and center.	Oct 7, 2021
GeneSetDb-class.Rd		GeneSetDb-class.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
SparrowResult-utilities.Rd		SparrowResult-utilities.Rd	Reorders parameters in seas() function to put the feature container f…	May 18, 2021
SparrowResult.Rd		SparrowResult.Rd	fixing some namespace and documentation stuff	May 6, 2021
addGeneSetMetadata.Rd		addGeneSetMetadata.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
all.equal.GeneSetDb.Rd		all.equal.GeneSetDb.Rd	Updated to use the GeneSetDb.MSigDB provider.	Sep 12, 2019
annotateGeneSetMembership.Rd		annotateGeneSetMembership.Rd	Reorders parameters in seas() function to put the feature container f…	May 18, 2021
calculateIndividualLogFC.Rd		calculateIndividualLogFC.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
collectionMetadata.Rd		collectionMetadata.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
combine-GeneSetDb-GeneSetDb-method.Rd		combine-GeneSetDb-GeneSetDb-method.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
combine-SparrowResult-SparrowResult-method.Rd		combine-SparrowResult-SparrowResult-method.Rd	Fix to getMSigGeneSetDb tests	May 3, 2021
conform.Rd		conform.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
conversion.Rd		conversion.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
convertIdentifiers.Rd		convertIdentifiers.Rd	fix docs	May 6, 2024
corplot.Rd		corplot.Rd	Introduces maximum size in the correlation stats of corplot	Oct 18, 2021
eigenWeightedMean.Rd		eigenWeightedMean.Rd	adds taxonomy ids to species_info outputs	Feb 18, 2025
examples.Rd		examples.Rd	More promotion of BiocSet of GeneSetDb as first point of call for end…	Oct 7, 2021
failWith.Rd		failWith.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
featureIdMap.Rd		featureIdMap.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
featureIds.Rd		featureIds.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
geneSet.Rd		geneSet.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
geneSetCollectionURLfunction.Rd		geneSetCollectionURLfunction.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
geneSetSummaryByGenes.Rd		geneSetSummaryByGenes.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
geneSets.Rd		geneSets.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
geneSetsStats.Rd		geneSetsStats.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
getKeggCollection.Rd		getKeggCollection.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
getMSigCollection.Rd		getMSigCollection.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
getPantherCollection.Rd		getPantherCollection.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
getReactomeCollection.Rd		getReactomeCollection.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
goseq.Rd		goseq.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
gsdScore.Rd		gsdScore.Rd	roxygenization	Oct 5, 2021
gskey.Rd		gskey.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
hasGeneSet.Rd		hasGeneSet.Rd	more markdownization	Oct 18, 2018
hasGeneSetCollection.Rd		hasGeneSetCollection.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
incidenceMatrix.Rd		incidenceMatrix.Rd	Seeking and destroying getMSigGeneSetDb from @examples	Oct 5, 2021
iplot.Rd		iplot.Rd	More work to bring BiocSet use front and center.	Oct 7, 2021
is.active.Rd		is.active.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
logFC.Rd		logFC.Rd	Reorders parameters in seas() function to put the feature container f…	May 18, 2021
mgheatmap.Rd		mgheatmap.Rd	roxygenization	Oct 5, 2021
mgheatmap2.Rd		mgheatmap2.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
msg.Rd		msg.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
ora.Rd		ora.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
p.matrix.Rd		p.matrix.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
randomGeneSetDb.Rd		randomGeneSetDb.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
renameCollections.Rd		renameCollections.Rd	update copyright	Jun 6, 2023
renameRows.Rd		renameRows.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
results.Rd		results.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
scale_rows.Rd		scale_rows.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
scoreSingleSamples.Rd		scoreSingleSamples.Rd	Removes dependence on reshape2 everywhere.	Oct 5, 2021
seas.Rd		seas.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
sparrow_methods.Rd		sparrow_methods.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
species_info.Rd		species_info.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
ssGSEA.normalize.Rd		ssGSEA.normalize.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
sub-GeneSetDb-ANY-ANY-ANY-method.Rd		sub-GeneSetDb-ANY-ANY-ANY-method.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
subset.GeneSetDb.Rd		subset.GeneSetDb.Rd	Upgrade to roxygen2 7.0.1	Nov 26, 2019
subsetByFeatures.Rd		subsetByFeatures.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
validateInputs.Rd		validateInputs.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
volcanoPlot.Rd		volcanoPlot.Rd	changes names()/values order or rename vector in renameCollections	Jun 6, 2023
volcanoStatsTable.Rd		volcanoStatsTable.Rd	Fix to getMSigGeneSetDb tests	May 3, 2021
zScore.Rd		zScore.Rd	Updates to codebase for bioconductor package submission	Sep 29, 2021
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