Transcription factor binding motif (TFBM) clustering
Align one single node with a cluster of (already aligned) motifs.
Align all the motifs, using as base the merge order of one hierarchical tree.
Align two already aligned clusters of motifs.
Align two single nodes.
Build distance matrix from a motif comparison table
Using a given agglomeration method, checks if the clusters will be aligned.
Identify the "central" or farthest leaves (motifs) between two clusters.
Assign one color to each cluster.
Convert 'hclust' tree to Newick format
Convert 'hclust' tree to Newick format.
Draw a heatmap of the input motifs, using the same distance tab and the same aggolmeration method.
Add gaps to the downstream end of the consensus
Traverse the tree in a bottom-up approach to separate the motifs clusters.
Given two sets of IDs, return the number of comparison from the given comparison table
Given two sets of IDs, return the number of comparison from the given comparison table
Extract the motif IUPAC consensus (or its reverse complement) from a reference table.
Extract the id of a motif from a reference table.
Extract the name of a motif from a reference table.
Counts the number of gaps ("-") in both ends of a consensus string.
Hierarchical clustering of the motifs.
Identify the order of the branches in the JSON tree, relative to the order of one hclust tree.
Invert the aligned consensus and orientation information for a group of aligned motifs.
Collect the nodes of each node of the tree.
Comparison matrix between 21 TFBM discovered by RSAT peak-motifs in Oct4 ChIP-seq peaks