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Showing results 1 to 10 of 2,731.


Function bdp [ChIPpeakAnno v3.6.5]
keywords
misc
title
obtain the peaks near bi-directional promoters
description
Obtain the peaks near bi-directional promoters. Also output percent of peaks near bi-directional promoters.
Function findOverlapsOfPeaks [ChIPpeakAnno v3.6.5]
keywords
misc
title
Find the overlapped peaks among two or more set of peaks.
description
Find the overlapping peaks for two or more (less than five) set of peak ranges.
Function findOverlappingPeaks [ChIPpeakAnno v3.6.5]
keywords
misc
title
Find the overlapping peaks for two peak ranges.
description
Find the overlapping peaks for two input peak ranges. This function is to keep the backward compatibility with previous versions for RangedData object. The new function findOverlapsOfPeaks is recommended. Convert RangedData to GRanges with toGRanges function.
Function oligoSummary [ChIPpeakAnno v3.6.5]
keywords
misc
title
Output a summary of consensus in the peaks
description
Calculate the z-scores of all combinations of oligonucleotide in a given length by Markove chain.
Function peakPermTest [ChIPpeakAnno v3.6.5]
keywords
misc
title
Permutation Test for two given peak lists
description
Performs a permutation test to seee if there is an association between two given peak lists.
Function GFF2RangedData [ChIPpeakAnno v3.6.5]
keywords
misc
title
Convert GFF format to RangedData
description
Convert GFF format to RangedData. This function will be depreciated. Use function toGRanges instead.
Function addAncestors [ChIPpeakAnno v3.6.5]
keywords
misc
title
Add GO IDs of the ancestors for a given vector of GO ids
description
Add GO IDs of the ancestors for a given vector of GO IDs leveraging GO.db package
Function addGeneIDs [ChIPpeakAnno v3.6.5]
keywords
misc
title
Add common IDs to annotated peaks such as gene symbol, entrez ID, ensemble gene id and refseq id.
description
Add common IDs to annotated peaks such as gene symbol, entrez ID, ensemble gene id and refseq 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 BED2RangedData [ChIPpeakAnno v3.6.5]
keywords
misc
title
Convert BED format to RangedData
description
Convert BED format to RangedData. This function will be depreciated.
Function toGRanges [ChIPpeakAnno v3.6.5]
keywords
misc
title
Convert dataset to GRanges
description
Convert UCSC BED format and its variants, such as GFF, or any user defined dataset such as RangedDate or MACS output file to GRanges