ChIPMunk motif discovery tool now comes in a single package with diChIPMunk, ready to process your ChIP-Seq, HT-SELEX, DNase footprints & similar data.
Our sequence-crunching rodents are now accompanied by SPRY-SARUS motif scanner, to apply discovered PWMs to look for motif hits in given sequence sets.
chipmunk.jar ChIPMunk v6d complied classes
userguide.pdf ChIPMunk v6 detailed user guide
chipmunk_src.jar ChIPMunk v6d java sources
chipmunk_peaksample.zip ChIPMunk peak fasta examples
chipmunk_scripts.zip ChIPMunk supporting scripts (ruby)Please, always use the latest versions provided at this page: v6d fixes single-strand r: mode for diChIPMunk.
Deep and wide digging for binding motifs in ChIP-Seq data. Kulakovskiy et al., 2010, PubMed
From binding motifs in ChIP-Seq data to improved models of transcription factor binding sites. Kulakovskiy et al., 2013, PubMed
Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data. Levitsky et al., 2014, PubMed
In case of any questions don't hesitate to contact [ivan-dot-kulakovskiy-at-gmail-dot-com].
This software is maintained by Ilya Vorontsov, Anastasia Soboleva and Ivan Kulakovskiy.