Allows to analyze, compare, and visualize next generation sequencing (NGS) data. CLC Genomics Workbench offers a complete and customizable solution for genomics, transcriptomics, epigenomics, and metagenomics. The software enables to generate custom workflows, which can combine quality control steps, adapter trimming, read mapping, variant detection, and multiple filtering and annotation steps into a pipeline.
Analyzes terabase-scale Hi-C datasets. Juicer allows users without a computational background to transform raw sequence data into normalized contact maps with one click. Juicer produces a hic file containing compressed contact matrices at many resolutions, facilitating visualization and analysis at multiple scales.
A computational model integrating Hi-C and histone mark ChIP-seq data to predict two important features of chromatin organization: chromatin interaction hubs and topologically associated domain (TAD) boundaries. HubPredictor accurately and robustly predicts these features across datasets and cell types. Cell-type specific histone mark information is required for prediction of chromatin interaction hubs but not for TAD boundaries. HubPredictor provides a useful guide for the exploration of chromatin organization.
A bioinformatics pipeline for the automated analysis of data generated by high-throughput chromatin conformation capture (HiC). The analysis workflow comprises steps of data formatting, genome alignment, quality control and filtering, identification of genome-wide chromatin interactions, visualization and statistics. An interactive browser enables visual inspection of interaction data and results.
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.
Provides users with a statistical pipeline for analysing chromosomal interactions data (Hi-C data). chromoR combines wavelet methods and a Bayesian approach for correction (bias and noise) and comparison (detecting significant changes between Hi-C maps) of Hi-C contact maps. In addition, it also support detection of change points in 1D Hi-C contact profiles. The chromoR package provides researchers with a means to analyse chromosomal interaction data using statistical bioinformatics, offering a new and comprehensive solution to this task.