diffHic statistics

info info

Citations per year

info

Popular tool citations

chevron_left Differential genomic interaction detection Normalization Bioinformatics workflows Heatmap generation Read alignment chevron_right
info

Tool usage distribution map

Tool usage distribution map
info info

Associated diseases

Associated diseases
Want to access the full stats & trends on this tool?

Protocols

diffHic specifications

Information


Unique identifier OMICS_09658
Name diffHic
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Sequence data
Input format BAM
Output data HDF5 files
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++, R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.12.1
Stability Stable
Requirements
limma, methods, stats, graphics, BiocGenerics, IRanges, GenomicRanges, Rsamtools, Matrix, utils, S4Vectors, GenomeInfoDb, Biostrings, grDevices, R(>=3.5), SummarizedExperiment, edgeR, locfit, Rcpp, BSgenome, BSgenome.Ecoli.NCBI.20080805, Rhtslib, rhdf5, InteractionSet, csaw
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Aaron Lun <>

Publication for diffHic

diffHic citations

 (2)
library_books

Software tools for visualizing Hi C data

2017
PMCID: 5290626
PMID: 28159004
DOI: 10.1186/s13059-017-1161-y

[…] data, but other transformations of the data can be visualized using the same set of tools. for example, statistical confidence measures, such as p-values produced by methods such as fit-hi-c [] or diffhic [], can be converted to a contact matrix format and then visualized using the tools reviewed here. hi-c data also can be used to infer the 3d structure of the chromatin (methods reviewed […]

library_books

Capturing genomic relationships that matter

2017
PMCID: 5346121
PMID: 28078515
DOI: 10.1007/s10577-016-9546-4

[…] provide context of interactions., an alternative analysis aims to identify functional interactions by characterising differential contacts between two cell types or conditions. homer, hibrowse and diffhic were developed for detecting differential interactions in hic data, built upon previous methods that were originally applied to identify differentially expressed genes in rna-seq data (e.g. […]


Want to access the full list of citations?
diffHic institution(s)
The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Melbourne, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC, Melbourne, Australia; Department of Mathematics and Statistics, The University of Melbourne, Parkville, VIC, Melbourne, Australia

diffHic reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review diffHic