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HIPPIE / High-throughput Identification Pipeline for Promoter Interacting Enhancer elements
A high-throughput identification pipeline for promoter interacting enhancer element to streamline the workflow from mapping raw Hi-C reads, identifying DNA-DNA interacting fragments with high confidence and quality control, detecting histone modifications and DNase hypersensitive enrichments in putative enhancer elements, to ultimately extracting possible intra- and inter-chromosomal enhancer-target gene relationships.
HiC-bench
Allows a comprehensive and reproducible analysis of Hi-C sequencing data. HiC-bench performs complete Hi-C analysis starting with the alignment of reads (fastq files) and ending with the annotation of specific interactions, their visualization and enrichment analysis. Hi-C pipeline integrates Anchoring Topological Domain (TAD) calling HiC-bench using published methods and your own algorithm and performs calculation of boundary scores using your own methods and existing ones. Every pipeline step is followed by summary statistics (when applicable) and visualization of the results. This allows quality control and facilitates troubleshooting. Furthermore, HiC-bench allows parameter exploration and comparison of different methods in a combinatorial fashion. This feature facilitates the design and execution of complex benchmark studies that may involve combinations of multiple parameter/tool choices in each step.
GenomeDISCO / Genome DIfferences between Smoothed COntact maps
Assesses the similarity of a pair of contact maps obtained from chromosome capture experiments. GenomeDISCO is designed for evaluating concordance and reproducibility of chromatin contact maps obtained from chromosome conformation capture experiments. It distinguishes biological replicates from different cell types with the desired sensitivity to sequencing depth, node and edge dropout noise, changes in domain boundaries and subtle differences in distance dependence.
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