We are analyzing https://link.springer.com/article/10.1186/s12859-015-0683-0.

Title:
diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data | BMC Bioinformatics
Description:
Background Chromatin conformation capture with high-throughput sequencing (Hi-C) is a technique that measures the in vivo intensity of interactions between all pairs of loci in the genome. Most conventional analyses of Hi-C data focus on the detection of statistically significant interactions. However, an alternative strategy involves identifying significant changes in the interaction intensity (i.e., differential interactions) between two or more biological conditions. This is more statistically rigorous and may provide more biologically relevant results. Results Here, we present the diffHic software package for the detection of differential interactions from Hi-C data. diffHic provides methods for read pair alignment and processing, counting into bin pairs, filtering out low-abundance events and normalization of trended or CNV-driven biases. It uses the statistical framework of the edgeR package to model biological variability and to test for significant differences between conditions. Several options for the visualization of results are also included. The use of diffHic is demonstrated with real Hi-C data sets. Performance against existing methods is also evaluated with simulated data. Conclusions On real data, diffHic is able to successfully detect interactions with significant differences in intensity between biological conditions. It also compares favourably to existing software tools on simulated data sets. These results suggest that diffHic is a viable approach for differential analyses of Hi-C data.
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Keywords {🔍}

data, pairs, diffhic, pubmed, article, hic, read, analysis, interactions, google, scholar, pair, biological, methods, cas, interaction, differential, normalization, conditions, biases, dis, package, genomic, chromatin, analyses, ligation, counts, number, results, edger, fig, genome, central, real, replicates, smyth, sequencing, filtering, additional, libraries, set, detect, alignment, differences, approach, study, restriction, space, size, detection,

Topics {✒️}

org/packages/release/bioc/html/rhdf5 org/packages/release/bioc/html/csaw org/packages/release/bioc/html/diffhic follow quasi-negative-binomial distributions user-friendly web-tool implemented command-line software suite chromatin conformation data gfp-overexpressing prostate cells org/smyth/pubs/qledgerpreprint org/smyth/pubs/robustebayespreprint high-throughput paired-end sequencing sequence-related genomic biases inter-chromosomal bin pairs multifactor srna-seq experiments negative marginal log-fcs biotin-labelled ligation products latest glm-based methods multi-purpose statistical analysis release chromatin complexes article download pdf decreasing marginal log-fcs fast gapped-read alignment cis-regulatory landscape cis-regulatory landscapes chromatin conformation intra-chromosomal bin pairs sequence alignment/map format interaction-specific biases due outward-facing read pairs marginal log-fold change assuming binomially-distributed counts low-abundance bin pairs references lieberman-aiden complex rna-seq experiments large-scale datasets open access license bin pair log-fc privacy choices/manage cookies eliminate cnv-driven differences cnv-based biases high-throughput sequencing reads macos programming language oncogene-mediated alterations remove genomic biases gene expression arrays dimensional chromatin interactome pre-splitting approach outperforms time-critical functions written diffhicproject home page rigorous analysis requires

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         Algorithms
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