Package index
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countPwmMatches() - Count the matches to a PWM within an XStringSet
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getClusterMatches()countClusterMatches() - Find matches from a PWM cluster within an XStringSet
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getPwmMatches() - Find all PWM matches within an XStringSet
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testClusterEnrich() - Test enrichment across a cluster of motifs using a background set of sequences
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testClusterPos() - Test positional bias motifs within a cluster
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testMotifEnrich() - Test motif enrichment using a background set of sequences
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testMotifPos() - Test for a Uniform Distribution across a set of best matches
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clusterMotifs() - Assign each motif to a cluster
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makeRMRanges() - Form a set of random, matching ranges for bootstrapping or permuting
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plotMatchPos() - Plot Motif Match Positions
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ar_er_peaks - A set of peaks with AR and ER detected
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ar_er_seq - Sequences from peaks with AR and ER detected
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ex_pfm - Example Position Frequency Matrices
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hg19_mask - Regions from hg19 with high N content
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zr75_enh - Candidate Enhancer Regions from ZR-75-1 Cells
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simMultiMotifs() - Simulate sequences with multiple motifs
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simSeq() - Simulate sequences using optional TFBMs