Sole-Search is an integrated peak-calling and analysis softwar which is available through a user-friendly interface and (i) converts raw data into a format for visualization on a genome browser, (ii) outputs ranked peak locations using a statistically based method that overcomes the significant problem of false positives, (iii) identifies the gene nearest to each peak, (iv) classifies the location of each peak relative to gene structure, (v) provides information such as the number of binding sites per chromosome and per gene and (vi) allows the user to determine overlap between two different experiments.
CHANCE (ChIP-seq Analytics and Confidence Estimation) is a software for assessing the quality of ChIP-seq experiments and providing feedback for the optimization of ChIP and library generation protocols.
CHANCE-HT is a ChIP-seq pre-processing software that filters samples with weak IP-strength, identifies heavily biased control experiments and under sequenced samples, detects batch effects, and normalizes large ensembles of ChIP-seq datasets.CHANCE-HT uses a parallel processing approach to normalize and filter large collections of ChIP-seq datasets in tandem.
ODIN is a HMM-based approach to detect and analyse differential peaks in pairs of ChIP-seq data. It is the first differential peak caller that performs genomic signal processing, peak calling and p-value calculation in an integrated framework.
Given a set of peaks from (biological or technical) replicates, MSPC combines the p-values of overlapping enriched regions: users can choose a threshold on the combined significance of overlapping peaks and set a minimum number of replicates where the overlapping peaks should be present. The method allows the “rescue” of weak peaks occuring in more than one replicate and outputs a new set of enriched regions for each replicate.