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.
Provides a simple graphical user interface for data pre-processing and a collection of higher-level data analysis tools implemented in R. Data pre-processing also supports a wide range of additional data types required for in-depth analysis of the Hi-C data (e.g. RNA-Seq, ChIP-Seq, and BS-Seq). Importantly, HiCdat is focused on the analysis of larger structural features of chromosomes, their correlation to genomic and epigenomic features, and on comparative studies. It uses simple input and output formats and can therefore easily be integrated into existing workflows or combined with alternative tools.
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.
Integrates experimental data obtained from different technologies to map the 3D structures of entire genomes. 3DGenome_FruitFly generates a large number of genome structures whose chromatin contacts are statistically consistent with those from the Hi-C data. It can be used for genomes of any organism, including mammalian genomes. The tool permits detailed analysis of the genome’s structural features, at high resolution and fully consistent with all experimental findings.
Aims to map global open chromatin interactions. OCEAN-C is a program allowing users to study open chromatin interactions and their relationship with gene regulation. This tool is developed for capturing interactions between open chromatin regions without relying on specific antibodies. It includes features for investigating changes in open chromatin conformations, such as promoter-enhancer interactions, that result in differential gene expression.
A technique to phase deletions to SNVs using only WGS and HiC sequencing from a single human donor. Phasing SNVs and deletions is similar to the haplotype assembly problem. InPhaDel addresses the question of determining if heterozygous deletions act in cis or trans with other heterozygous variants. We formulate the task as a multi-class classification problem where deletions can be phased to either chromosome (pA or pB), homozygous or unsupported by the read data. We used Nearest Neighbors, SVM and Random Forest learning methods to solve this problem.
Assess the influences of genomic features such as DNA-binding proteins and functional elements on topological domain borders. HiCfeat is an R package offering a multiple logistic regression that can be easily accommodate interactions between genomic features to assess the impact of co-occurrences on domain borders. This model outperforms enrichment test and nonparametric models in the identification of known and suspected architectural proteins.
A generalized linear regression with higher-order interaction terms to assess the influences of genomic features such as DNA-binding proteins and functional elements on long-range contacts from Hi-C experiments.
A web server for analyzing spatial contact of chromosomes from the publicly available Hi-C data. ChromContact is designed to be simple and easy to use. By specifying a locus of interest, ChromContact calculates contact profiles and generates links to the UCSC Genome Browser, enabling users to visually examine the contact information with various annotations. ChromContact provides wide-range of molecular biologists with a user-friendly means to access high-resolution Hi-C data. One of the possible applications of ChromContact is investigating novel long-range promoter-enhancer interactions. This facilitates the functional interpretation of statistically significant markers identified by GWAS or ChIP-seq peaks that are located far from any annotated genes.
Allows users to analyze how pathways and genetic interactions rewire over time. MODIFI identifies and characterizes differential interactions. This two-factor linear model can estimate the predictive strength and influence of time and differential compound treatment on pi-score. This estimation can be described as the slope by which an interaction changes (strengthens or weakens) over time.
Reconstructs 3D organizations of chromosomes. GEM-FISH is a divide-and-conquer based method that systematically integrates e fluorescent in situ hybridization (FISH) data with both high chromosome contact map (Hi-C) data and the prior biophysical knowledge of a polymer model. The final 3D models reconstructed by this method can also capture the spatial proximity of loop loci and the colocalization of loci belonging to the same subcompartments.
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