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3D-GNOME / 3D GeNOme Modeling Engine
Allows a user without any programing experience to generate 3D structures from 3C data with minimal effort, and simply requires any modern web browser to access and use. 3D-GNOME provides a web-based, interactive 3D viewer to visualize and analyze the resulting 3D structure, and includes options for the user to upload genomic annotation data to overlay on the structure. In addition to the 3D structure, 3D-GNOME provides a variety of other analysis tools, including 1D arc representations and 2D heatmap representations of the data.
An easy-to-use and complete analysis pipeline to process both bridge-linker and half-linker ChIA-PET data from raw sequencing reads to significant chromatin loop calls. ChIA-PET can detect chromatin loops with a significantly higher sensitivity and reproducibility than the existing pipeline at the same false discovery rate. Mismatches are allowed at the linker trimming step, which rescues a large portion of pair-end tags (PETs). Multi-threading is supported to speed up the processing time. Quality control measures are supported at different steps of the ChIA-PET analysis. When phased genotype data are available, ChIA-PET is also able to detect allele-specific chromatin loops.
A complete ChIA-PET data analysis pipeline that provides statistical confidence estimates for interactions and corrects for major sources of bias including differential peak enrichment and genomic proximity. Comparison to the existing software packages, ChIA-PET Tool and ChiaSig, revealed that Mango interactions exhibit much better agreement with high-resolution Hi-C data. Importantly Mango executes all steps required for processing ChIA-PET data sets whereas ChiaSig only completes 20% of the required steps.
Identifies differential DNA looping between samples. diffloop provides a suite of tools to uncover differential loops in DNA with statistical rigor and integrate other bioinformatics data. It aims to subsetting, visualizing, annotating, and statistically analyzing the results of one or more ChIA-PET experiments or other assays that infer chromatin loops. The analyses show how differences in chromatin accessibility, DNA methylation, histone modifications, and cohesin localization correlate with differences in DNA looping, and how looping relates to differences in gene expression and cellular phenotypes.
Offers functions for the analysis of chromatin interactions using MC_DIST model (one sample problem), Two-Step model and One-Step model. MDM provides: (i) a function MCDIST to detect ture chromatin interactions using a dataset obtained from a chromatin looping experiment, (ii) a function MDTS to peoform the second step of the Two-Step model for detecting chromatin interactions with different intensities in two samples, and (iii) a function MDOS to peoform the One-Step model for detecting chromatin interactions with different intensities in two samples.
QuIN / Query tool for Interaction Networks
A web-based application for visualizing, annotating, and querying chromatin interactions derived from technologies such as ChIA-PET or HiC. QuIN enables: 1) building and visualizing chromatin interaction networks, 2) annotating networks with user-provided private and publicly available functional genomics and interaction datasets, 3) querying network components based on gene name or chromosome location, and 4) utilizing network based measures to identify and prioritize critical regulatory targets and their direct and indirect interactions.
Serves for analyzing ChIA-PET data that integrates chromatin interaction discovery with the identification of interaction anchor points. SPROUT allows analysis by modeling the empirical distribution of read positions around interaction anchors. This tool includes features for determining the positions of anchors and assigning pairs of reads to anchors. Moreover, it models read-pair data with a mixture over distributions describing the generation of self-ligation pairs and inter-ligation pairs.
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