Assists researchers to analyze entanglements of chromosomes. KnotGenome detects and characterizes knots in single chromosomes, as well as links between chromosomes. It contains features for: (1) analyzing polymers composed of up to 5000 beads, (2) identifying composite knots, (iii) offering four different types of closures, (iv) using the Gaussian linking number (GLN) to identify the entangled regions and (v) estimating the robustness of the links via relaxation.
Utilizes chromatin contact maps to identify translocations in cancer cell lines. HiCtrans is a computational method scans fixed-size resolution inter-chromosomal contact maps of each chromosome pair for potential translocations using change-point statistics. This pipeline starts with performing binary segmentation independently on each row and column of an inter-chromosomal matrix. It then aggregates the change points identified from the perspective of each chromosome to determine rectangular boxes of contact enrichment with respect to the overall inter-chromosomal matrix.
Utilizes chromatin contact maps to identify copy number variations (CNVs) in cancer cell lines. HiCnv is a computational method that works on contact counts at the single restriction enzyme (RE) fragment level in order to leverage Hi-C data at its highest possible and native resolution. This method first computes 1D read coverage for each RE fragment, followed by normalization, smoothing and segmentation. Then, it processes for refinement of their breakpoint coordinates (segment ends) and assignment of their CNV labels.
Measures local chromosomal structural similarity. localtadsim discovers similar regions of topologically associating domain (TAD) structures. It can be used to assess the similarity of chromosome structure across all pairwise combinations of samples. This tool takes as input two lists of TADs from different sample to find the sub-intervals in which the two TAD lists are significantly similar.
Represents epigenomic data by k-mer words associated with epigenomic mark. BROCKMAN enables the investigation of variation in k-mer occupancy across single cells as a basis for distinguishing different cell types, states, and treatments. It is based on matrix factorization and dimensionality reduction. This tool can be used to find differentially active transcription factors (TFs) and to interpret TF-TF interactions.
Makes annotations and displays interacting chromatin regions. HiCAGE includes processed interaction regions derived from 3C-based data with genomic annotations and assigns genes by proximity. It can sort expression lists by interaction class enabling subsequent gene-ontology investigation. This tool is useful for the visualization of reorganization of chromatin structure and gene expression changes on a whole genome level.
Allows users to detect statistical significance interactions in HiChIP data or PLAC-seq data. FitHiChIP provides an application able to generate four types of interactions among fixed size genomic segments coupled to a normalization technique. This program also includes an utility to create paired-end alignment files and can be run on either a computational cluster or a laptop.
Allows users to work on High Chromosome Contact map (Hi-C) analysis at dynamic scales. SHAMAN is useful to produce randomized matrices conserving empirical number of contacts by restriction fragment and the empirical distribution of genomic distances over contacts. It permits user to reanalyze Hi-C data on mouse embryonic stem cells and human cancer cell lines.
Assists users for chromosome flexibility analysis. FRI_chrFle is a flexibility-rigidity index (FRI) based model. Based on the Hi-C data, it permits to evaluate a flexibility index for each locus. This model provides a direct link between the chromosome packing density with chromosome flexibility. Inter-chromosome information can be easily incorporated into the flexibility evaluation.
Allows to explore genome organization. GeSICA calculates a simple logged ratio to efficiently segment the human genome into regions with two distinct states that correspond to rich and poor functional element states. It quantifies the degree of chromatin openness by using the principle that the assumption that random short-range DNA interactions would be easier to detect in open chromatin environments, and that the calculated interaction ratio could be regarded as an index.
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