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Showing results 21 to 30 of 2,971.


Function annotatePeakInBatch [ChIPpeakAnno v3.6.5]
keywords
misc
title
Obtain the distance to the nearest TSS, miRNA, and/or exon for a list of peaks
description
Obtain the distance to the nearest TSS, miRNA, exon et al for a list of peak locations leveraging IRanges and biomaRt package
Function assignChromosomeRegion [ChIPpeakAnno v3.6.5]
keywords
misc
title
Summarize peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTR
description
Summarize peak distribution over exon, intron, enhancer, proximal promoter, 5 prime UTR and 3 prime UTR
Function condenseMatrixByColnames [ChIPpeakAnno v3.6.5]
keywords
misc
title
Condense matrix by colnames
description
Condense matrix by colnames
Function convert2EntrezID [ChIPpeakAnno v3.6.5]
keywords
misc
title
Convert other common IDs to entrez gene ID.
description
Convert other common IDs such as ensemble gene id, gene symbol, refseq id to entrez gene ID leveraging organism annotation dataset. For example, org.Hs.eg.db is the dataset from orgs.Hs.eg.db package for human, while org.Mm.eg.db is the dataset from the org.Mm.eg.db package for mouse.
Function findEnhancers [ChIPpeakAnno v3.6.5]
keywords
misc
title
Find possible enhancers depend on DNA interaction data
description
Find possible enhancers by data from chromosome conformation capture techniques such as 3C, 5C or HiC.
Function featureAlignedSignal [ChIPpeakAnno v3.6.5]
keywords
misc
title
extract signals in given ranges
description
extract signals in the given feature ranges
Function getEnrichedPATH [ChIPpeakAnno v3.6.5]
keywords
misc
title
Obtain enriched PATH that near the peaks
description
Obtain enriched PATH that are near the peaks using path package such as reactome.db and path mapping package such as org.Hs.db.eg to obtain the path annotation and using hypergeometric test (phyper) and multtest package for adjusting p-values
Function featureAlignedDistribution [ChIPpeakAnno v3.6.5]
keywords
misc
title
plot distribution in given ranges
description
plot distribution in the given feature ranges
Function binOverFeature [ChIPpeakAnno v3.6.5]
keywords
misc
title
Aggregate peaks over bins from the TSS
description
Aggregate peaks over bins from the feature sites.
Function featureAlignedHeatmap [ChIPpeakAnno v3.6.5]
keywords
misc
title
Heatmap representing signals in given ranges
description
plot heatmap in the given feature ranges