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Showing results 11 to 20 of 2,976.


Function translatePattern [ChIPpeakAnno v3.6.5]
keywords
misc
title
translate pattern from IUPAC Extended Genetic Alphabet to regular expression
description
translate pattern containing the IUPAC nucleotide ambiguity codes to regular expression. For example,Y->[C|T], R-> [A|G], S-> [G|C], W-> [A|T], K-> [T|U|G], M-> [A|C], B-> [C|G|T], D-> [A|G|T], H-> [A|C|T], V-> [A|C|G] and N-> [A|C|T|G].
Function getAnnotation [ChIPpeakAnno v3.6.5]
keywords
misc
title
Obtain the TSS, exon or miRNA annotation for the specified species
description
Obtain the TSS, exon or miRNA annotation for the specified species using the biomaRt package
Function getEnrichedGO [ChIPpeakAnno v3.6.5]
keywords
misc
title
Obtain enriched gene ontology (GO) terms that near the peaks
description
Obtain enriched gene ontology (GO) terms based on the features near the enriched peaks using GO.db package and GO gene mapping package such as org.Hs.db.eg to obtain the GO annotation and using hypergeometric test (phyper) and multtest package for adjusting p-values
Function mergePlusMinusPeaks [ChIPpeakAnno v3.6.5]
keywords
misc
title
Merge peaks from plus strand and minus strand
description
Merge peaks from plus strand and minus strand within certain distance apart, and output merged peaks as bed format.
Function preparePool [ChIPpeakAnno v3.6.5]
keywords
misc
title
prepare data for permutation test
description
prepare data for permutation test peakPermTest
Function reCenterPeaks [ChIPpeakAnno v3.6.5]
keywords
misc
title
re-center the peaks
description
Create a new list of peaks based on the peak centers of given list.
Function pie1 [ChIPpeakAnno v3.6.5]
keywords
misc
title
Pie Charts
description
Draw a pie chart with percentage
Function addMetadata [ChIPpeakAnno v3.6.5]
keywords
misc
title
Add metadata of the GRanges objects used for findOverlapsOfPeaks
description
Add metadata to to overlapping peaks after calling findOverlapsOfPeaks.
Function getVennCounts [ChIPpeakAnno v3.6.5]
keywords
misc
title
Obtain Venn Counts for Venn Diagram, internal function for makeVennDigram
description
Obtain Venn Counts for peak ranges using chromosome ranges or feature field, internal function for makeVennDigram
Function peaksNearBDP [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.