Motif2Site - Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions
Detect binding sites using motifs IUPAC sequence or bed coordinates and ChIP-seq experiments in bed or bam format. Combine/compare binding sites across experiments, tissues, or conditions. All normalization and differential steps are done using TMM-GLM method. Signal decomposition is done by setting motifs as the centers of the mixture of normal distribution curves.
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softwaresequencingchipseqdifferentialpeakcallingepigeneticssequencematching
4.30 score 5 scripts 406 downloadsSite2Target - An R package to associate peaks and target genes
Statistics implemented for both peak-wise and gene-wise associations. In peak-wise associations, the p-value of the target genes of a given set of peaks are calculated. Negative binomial or Poisson distributions can be used for modeling the unweighted peaks targets and log-nromal can be used to model the weighted peaks. In gene-wise associations a table consisting of a set of genes, mapped to specific peaks, is generated using the given rules.
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annotationchipseqsoftwareepigeneticsgeneexpressiongenetarget
4.00 score 6 scripts 240 downloads