diffHic
diffHic is an advanced software package for analyzing differential interactions in Hi-C data, providing a more nuanced understanding of chromatin conformation changes across various biological conditions. It facilitates the entire analysis pipeline, from read pair alignment and processing to normalizing biases and statistical testing for significant interaction differences using the edgeR framework. With capabilities for handling low-abundance events and integrating various visualization options, diffHic offers a comprehensive solution for researchers seeking to uncover the dynamic nature of chromatin interactions.
Topic
Sequencing;Omics
Detail
Operation: Standardisation and normalisation;Clustering
Software interface: Command-line user interface,Library
Language: R
License: The GNU General Public License v3.0
Cost: Free
Version name: 1.34.0
Credit: The Walter and Eliza Hall Institute of Medical Research, The University of Melbourne, and the National Health and Medical Research Council.
Input: Sequence [BAM]
Output: Hierarchy [Binary format] [Image format], Plot [Binary format] [Image format]
Contact: Aaron Lun infinite.monkeys.with.keyboards@gmail.com
Collection: -
Maturity: Stable
Publications
- diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data.
- Lun AT and Smyth GK. diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data. diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data. 2015; 16:258. doi: 10.1186/s12859-015-0683-0
- https://doi.org/10.1186/s12859-015-0683-0
- PMID: 26283514
- PMC: PMC4539688
Download and documentation
Source: https://bioconductor.org/packages/release/bioc/src/contrib/diffHic_1.34.0.tar.gz
Documentation: https://bioconductor.org/packages/release/bioc/manuals/diffHic/man/diffHic.pdf
Home page: http://bioconductor.org/packages/release/bioc/html/diffHic.html
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