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A Motif object contains general motif characteristics and and details of motif match
● Data Source:
BioConductor
● Keywords:
● Alias: Motif-class, class:Motif
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findMotif
(Package: motifRG) :
De-novo discovery of distriminative motifs
The function searches motifs that discriminate the given foregound and background sequences.
● Data Source:
BioConductor
● Keywords:
● Alias: findMotif
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1 images
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findMotifFasta
(Package: motifRG) :
Wrapper function for findMotif using fasta input
Perform motif search on two input fasta files. This is a wrapper function for findMotif
● Data Source:
BioConductor
● Keywords:
● Alias: findMotifFasta
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0 images
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findMotifFgBg
(Package: motifRG) :
Wrapper function for findMotif using two sequence datasets
Perform motif search on two sequence datasets. This is a wrapper function for findMotif.
● Data Source:
BioConductor
● Keywords:
● Alias: findMotifFgBg
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0 images
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getSequence
(Package: motifRG) :
Fetch genomic sequences from GRanges Object
The function fetch genomic sequences given the coordinates and strand informaton
● Data Source:
BioConductor
● Keywords:
● Alias: getSequence
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create a latex table to be embedded in a latex document
● Data Source:
BioConductor
● Keywords:
● Alias: motifHtmlTable, motifLatexTable
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0 images
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plotMotif
(Package: motifRG) :
plot motif sequence matches
plot aligned sequences, revealing the independent position specificity and dependency among adjacent positions.
● Data Source:
BioConductor
● Keywords:
● Alias: plotMotif
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3 images
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refinePWMMotif
(Package: motifRG) :
create a PWM (Position Weight Model) model given a initial set of motif matches and
Create a PWM model given a initial set of motif matches and input sequences
● Data Source:
BioConductor
● Keywords:
● Alias: refinePWMMotif
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3 images
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refinePWMMotifExtend
(Package: motifRG) :
create an extended PWM (Position Weight Model) model given a initial set of motif matches and
Create an extended PWM model given a initial set of motif matches and input sequences
● Data Source:
BioConductor
● Keywords:
● Alias: refinePWMMotifExtend
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0 images
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summaryMotif
(Package: motifRG) :
summarize a list of motifs
Create a summary table of a list of motifs found by findMotif
● Data Source:
BioConductor
● Keywords:
● Alias: summaryMotif
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0 images
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