PeakRanger detects enriched regions from ChIP-Seq experiments and also detect summits within these regions. The software is faster than most existing peak callers while consuming less memories.
::DEVELOPER
developed in Dr.Lincoln Stein’s lab at OICR and is now in continual development at Dr.Helen Hobbs’s lab of the McDermott Center of UT Southwestern.
DROMPA (DRaw and Observe Multiple enrichment Profiles and Annotation) is cost-effient program for peak-calling and visualization for ChIP-seq analysis. DROMPA outputs the protein binding profile map (ChIP-reads distribution and ChIP/control enrichment profile) with genomic annotation specified in pdf or png format, which can be easily handled and processed by users with little bioinformatics background. DROMPA has an associated program named parse2wig, which preprocesses the map file into wig files. This two-step procedure can drastically reduce the computational memory and time required, which makes enable to analyze large-scale ChIP-seq data (e.g., more than 10 human samples and/or multiple executions for each sample with trial-and-error) on a conventional desktop computer.
DROMPAplus is an update of DROMPA3. It is written in C++ and runs from a single launch command on conventional Linux systems.
GEM (Genome wide Event finding and Motif discovery) is a software tool to study protein-DNA interaction using ChIP-Seq/ChIP-exo data. GEM resolves ChIP data into explanatory motifs and binding events at unsurpassed spatial resolution by linking binding event discovery and motif discovery with positional priors in the context of a generative model of ChIP data and genome sequence.
Yuchun Guo, Georgios Papachristoudis, Robert C Altshuler, Georg K Gerber, Tommi S Jaakkola, David K Gifford & Shaun Mahony, Discovering homotypic binding events at high spatial resolution.
Bioinformatics. 2010 Dec 15;26(24):3028-34. Epub 2010 Oct 21. PMID: 20966006.
W-ChIPeaks employs a probe-based or bin-based enrichment threshold to define peaks and applies statistical methods to control the false discovery rate for identified peaks.