Peak calling software tools | ChIP sequencing data analysis

Performs peak finding and downstream data analysis for next-generation sequencing analysis. HOMER affords several tools and methods to make use of ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and other types of functional genomics sequencing data sets. This software offers support to UCSC visualization, peaks annotation, quantification of transcripts and repeats or differential features, enrichment and expression.

Serves as a transcriptome reconstruction method. Scripture is able to reconstruct a mammalian transcriptome with no prior knowledge of gene annotations. It exploits longer reads that span splice junctions to link discontiguous (spliced) segments. This software identifies short but strongly expressed transcripts, lower transcripts with aggregate evidence and precise gene structures for most of found lincRNA loci.

Provides a range of functionalities for ChIP data analyses. CisGenome allows visualization, data normalization, peak detection, false discovery rate (FDR) computation, gene-peak association, and sequence and motif analysis. The software can handle data from two types of designs common in ChIP-seq experiments. The basic functionalities of CisGenome can be used in combination to address several different biological questions.

Allows analysis of ChIP-seq and other functional sequencing data. SPP is an R package providing a data processing pipeline optimized for detection of localized protein binding positions from unpaired sequence reads. This software can examine the saturation level of detected binding position to determine the amount of additional sequencing that may be necessary. It assesses also saturation properties and determines minimal saturated enrichment ratio (MSER).

Identifies peak regions in ChIP-Seq datasets that correspond to sites of transcription factor binding. PeakSeq scores the results of ChIP-Seq experiments by compensating for the mappability map and comparing against a normalized matching control dataset. This method was developed for use with tag sequence data from the Illumina Genome Analyzer platform. It can also be used to identify broader regions of binding that show significant enrichment relative to control.