FitHiChIP: Identification of significant chromatin contacts from HiChIP data

Research datakeyboard_double_arrow_right Dataset 08 Jul 2019 English Publisher:ZenodoFunded by:NIH | Defining interaction quan..., NIH | Research Resources: Epige..., NIH | Defining interaction quan...

Authors: Sourya Bhattacharyya; Chandra, Vivek; Pandurangan Vijayanand; Ay, Ferhat;

doi: 10.5281/zenodo.3255048 , 10.5281/zenodo.3255047

FitHiChIP: Identification of significant chromatin contacts from HiChIP data

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Abstract

FitHiChIP is a computational method for identifying chromatin contacts among regulatory regions such as enhancers and promoters from HiChIP/PLAC-seq data. Functionalities of FitHiChIP include: 1) Calling significant interactions / loops / contacts from a HiChIP / PLAC-seq data 2) Identifying peaks (enriched segments) from a HiChIP data (i.e. HiChIP peak caller) 3) Finding differential loops among non-differential loci between two different categories of HiChIP samples, each with one or more replicates. GitHub page: github.com/ay-lab/FitHiChIP Documentation: https://ay-lab.github.io/FitHiChIP/ Citation: Please check the above documentation regarding citation of FitHiChIP About this repository: All the data and results provided here correspond to the published manuscript. The file Data_Summary.xlsx summarizes for each figure, corresponding tables storing the related datasets.

Related Organizations

University of California, San Diego
United States
La Jolla Institute For Allergy & Immunology
United States

Keywords

Significant interaction, PLAC-seq, Bias regression, Differential Contact, HiChIP, Genomic Distance

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