4DNvestigator: time series genomic data analysis toolbox
Data on genome organization and output over time, or the 4D Nucleome (4DN), require synthesis for meaningful interpretation. Development of tools for the efficient integration of these data is needed, especially for the time dimension. We present the ‘4DNvestigator’, a user-friendly network-based to...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2021-01-01
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| Series: | Nucleus |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/19491034.2021.1910437 |
| _version_ | 1818700135715045376 |
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| author | Stephen Lindsly Can Chen Sijia Liu Scott Ronquist Samuel Dilworth Michael Perlman Indika Rajapakse |
| author_facet | Stephen Lindsly Can Chen Sijia Liu Scott Ronquist Samuel Dilworth Michael Perlman Indika Rajapakse |
| author_sort | Stephen Lindsly |
| collection | DOAJ |
| description | Data on genome organization and output over time, or the 4D Nucleome (4DN), require synthesis for meaningful interpretation. Development of tools for the efficient integration of these data is needed, especially for the time dimension. We present the ‘4DNvestigator’, a user-friendly network-based toolbox for the analysis of time series genome-wide genome structure (Hi-C) and gene expression (RNA-seq) data. Additionally, we provide methods to quantify network entropy, tensor entropy, and statistically significant changes in time series Hi-C data at different genomic scales. |
| first_indexed | 2024-12-17T15:00:08Z |
| format | Article |
| id | doaj.art-336682a3e90f4bca9077f566359d1f71 |
| institution | Directory Open Access Journal |
| issn | 1949-1034 1949-1042 |
| language | English |
| last_indexed | 2024-12-17T15:00:08Z |
| publishDate | 2021-01-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Nucleus |
| spelling | doaj.art-336682a3e90f4bca9077f566359d1f712022-12-21T21:43:56ZengTaylor & Francis GroupNucleus1949-10341949-10422021-01-01121586410.1080/19491034.2021.191043719104374DNvestigator: time series genomic data analysis toolboxStephen Lindsly0Can Chen1Sijia Liu2Scott Ronquist3Samuel Dilworth4Michael Perlman5Indika Rajapakse6University of MichiganUniversity of MichiganMIT-IBM Watson AI Lab, IBM ResearchUniversity of MichiganiReprogramUniversity of WashingtonUniversity of MichiganData on genome organization and output over time, or the 4D Nucleome (4DN), require synthesis for meaningful interpretation. Development of tools for the efficient integration of these data is needed, especially for the time dimension. We present the ‘4DNvestigator’, a user-friendly network-based toolbox for the analysis of time series genome-wide genome structure (Hi-C) and gene expression (RNA-seq) data. Additionally, we provide methods to quantify network entropy, tensor entropy, and statistically significant changes in time series Hi-C data at different genomic scales.http://dx.doi.org/10.1080/19491034.2021.19104374dncentralityentropynetworkstime series |
| spellingShingle | Stephen Lindsly Can Chen Sijia Liu Scott Ronquist Samuel Dilworth Michael Perlman Indika Rajapakse 4DNvestigator: time series genomic data analysis toolbox Nucleus 4dn centrality entropy networks time series |
| title | 4DNvestigator: time series genomic data analysis toolbox |
| title_full | 4DNvestigator: time series genomic data analysis toolbox |
| title_fullStr | 4DNvestigator: time series genomic data analysis toolbox |
| title_full_unstemmed | 4DNvestigator: time series genomic data analysis toolbox |
| title_short | 4DNvestigator: time series genomic data analysis toolbox |
| title_sort | 4dnvestigator time series genomic data analysis toolbox |
| topic | 4dn centrality entropy networks time series |
| url | http://dx.doi.org/10.1080/19491034.2021.1910437 |
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