Name
Title | ||
|---|---|---|
HiC-spector: a matrix library for spectral and reproducibility analysis of Hi-C contact maps. |
Abstract | ||
|---|---|---|
Genome-wide proximity ligation based assays like Hi-C have opened a window to the 3D organization of the genome. In so doing, they present data structures that are different from conventional 1D signal tracks. To exploit the 2D nature of Hi-C contact maps, matrix techniques like spectral analysis are particularly useful. Here, we present HiC-spector, a collection of matrix-related functions for analyzing Hi-C contact maps. In particular, we introduce a novel reproducibility metric for quantifying the similarity between contact maps based on spectral decomposition. The metric successfully separates contact maps mapped from Hi-C data coming from biological replicates, pseudo-replicates and different cell types. Availability and Implementation: Source code in Julia and Python, and detailed documentation is available at https://github. com/gersteinlab/HiC- spector. Contact: koonkiu. yan@ gmail. com or mark@ gersteinlab. org Supplementary information: Supplementary data are available at Bioinformatics online. |
Year | DOI | Venue |
|---|---|---|
2017 | 10.1093/bioinformatics/btx152 | BIOINFORMATICS |
Field | DocType | Volume |
Data structure,Reproducibility,Source code,Matrix (mathematics),Computer science,Matrix decomposition,Bioinformatics,Spectral analysis | Journal | 33 |
Issue | ISSN | Citations |
14 | 1367-4803 | 3 |
PageRank | References | Authors |
0.61 | 1 | 5 |
Name | Order | Citations | PageRank |
|---|---|---|---|
| Koon-Kiu Yan | 1 | 80 | 5.94 |
| Galip Gürkan Yardımcı | 2 | 8 | 2.93 |
| Chengfei Yan | 3 | 22 | 2.79 |
| William S. Noble | 4 | 29 | 4.00 |
| Mark Gerstein | 5 | 8 | 6.72 |