Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions

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Documentation for package ‘Motif2Site’ version 1.12.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

Bed2Granges	Read a bed file as Genomic Ranges
combine2Table	Combine all IP and Input count table files
combineMotifFiles	Combine motif bed files into a combined ranges
combineTestResults	Combine count Table and statistics table
compareBedFiless2UserProvidedRegions	Compare a set of bed files to a user provided regions set
CompareBeds2GivenRegions	Compare a set of bed files to a provided regions set
CompareMotifs2GivenRegions	Comparison motifs locations to a given regions set
compareMotifs2UserProvidedRegions	Compare a set of motifs to a user provided regions set
computeFoldEnrichment	compute fold enrichment values for an experiment
data	Synthetic datasets used in the package
decomposeBindingSignal	Decompose binding signal among accepted motifs
DeleteMultipleFiles	Delete a vector of files
deriveHeuristicBindingDistribution	build heurisitc distribution around the binding sites
DetectBindingSites	Detect binding sites from motif
DetectBindingSitesBed	Detect binding sites from bed motif input
DetectBindingSitesMotif	Detect binding sites from sequence motif sequence and mismatchNumber
DetectFdrCutoffBH	FDR cut-off detection Benjamini Hochberg method
findMotifs	Find motif instances with a certain mismatch number
fitKernelDensity	Fit a kernel density distribution to the obersever heuristic distribution
generate1ntBedAlignment	Convert bam and bed files to 1 nucleotide bed
Motif2Site	Detect and Recenter binding sites from ChIP-seq experiments
motifBindingNegativeBinomialCount	Model IP and Input count values with negative Binomal
motifChipCount	count short reads related to each motif for a given ChIPseq file
motifCount	count short reads around motifs for all ChIP-seq experiments
motifTablePreProcess	Process count data and perform negative binomial test
NegativeBinomialTestWithReplicate	Negative binomial test of binding using all replicates
pairwisDifferential	Detect differential motifs
quiet	Suppress messages generated by in external package
recenterBindingSitesAcrossExperiments	Combine binding sites across experiments
removeNonBellShapedMotifs	Remove non-bell shpape motifs prior to binding signal decomposition
strongestMotif	Returns the motif with the highest count