homer

From the website: "Homer includes several motif databases that are used to help annotate
results and conduct searches for known motifs.  HOMER contains a custom motif
database based on independent analysis of mostly ChIP-Seq data sets which is
heavily utilized in the software." See <url>http://homer.salk.edu/homer/motif/motifDatabase.html</url>
for more information on how these files were generated, and Homer's sources.

datasets

We introduce motifbreakR, which allows the biologist to
        judge in the first place whether the sequence surrounding the
        polymorphism is a good match, and in the second place how much
        information is gained or lost in one allele of the polymorphism
        relative to another. MotifbreakR is both flexible and
        extensible over previous offerings; giving a choice of
        algorithms for interrogation of genomes with motifs from public
        sources that users can choose from; these are 1) a weighted-sum
        probability matrix, 2) log-probabilities, and 3) weighted by
        relative entropy. MotifbreakR can predict effects for novel or
        previously described variants in public databases, making it
        suitable for tasks beyond the scope of its original design.
        Lastly, it can be used to interrogate any genome curated within
        Bioconductor (currently there are 22).

Simon Gert Coetzee

motifbreakR

A Package For Predicting The Disruptiveness Of Single Nucleotide
        Polymorphisms On Transcription Factor Binding Sites

homer function

Heinz S, Benner C, Spann N, Bertolino E et al. (2010 May 28) Simple Combinations
  of Lineage-Determining Transcription Factors Prime cis-Regulatory
  Elements Required for Macrophage and B Cell Identities. Mol Cell, <b>38(4):576-589</b>.
  PMID: <href>http://www.ncbi.nlm.nih.gov/sites/entrez?Db=Pubmed&term=20513432[UID]</href>{20513432}

homer: MotifDb object containing motif information from motif databases included in HOMER.

Description

Usage

Arguments

Value

source

Details

See Also

Examples