R N Ramirez1, K Bedirian1,2, S M Gray1, A Diallo1. 1. Department of Immunology, Harvard Medical School, Boston, MA, 02115, USA. 2. Electrical and Computer Engineering Department, American University of Beirut, Beirut, Lebanon.
Abstract
MOTIVATION: Visualization of multiple genomic data generally requires the use of public or commercially hosted browsers. Flexible visualization of chromatin interaction data as genomic features and network components offer informative insights to gene expression. An open source application for visualizing HiC and chromatin conformation-based data as 2D-arcs accompanied by interactive network analyses is valuable. RESULTS: DNA Rchitect is a new tool created to visualize HiC and chromatin conformation-based contacts at high (Kb) and low (Mb) genomic resolutions. The user can upload their pre-filtered HiC experiment in bedpe format to the DNA Rchitect web app that we have hosted or to a version they themselves have deployed. Using DNA Rchitect, the uploaded data allows the user to visualize different interactions of their sample, perform simple network analyses, while also offering visualization of other genomic data types. The user can then download their results for additional network functionality offered in network based programs such as Cytoscape. AVAILABILITY AND IMPLEMENTATION: DNA Rchitect is freely available both as a web application written primarily in R available at http://shiny.immgen.org/DNARchitect/ and as an open source released under an MIT license at: https://github.com/alosdiallo/DNA_Rchitect.
MOTIVATION: Visualization of multiple genomic data generally requires the use of public or commercially hosted browsers. Flexible visualization of chromatin interaction data as genomic features and network components offer informative insights to gene expression. An open source application for visualizing HiC and chromatin conformation-based data as 2D-arcs accompanied by interactive network analyses is valuable. RESULTS: DNA Rchitect is a new tool created to visualize HiC and chromatin conformation-based contacts at high (Kb) and low (Mb) genomic resolutions. The user can upload their pre-filtered HiC experiment in bedpe format to the DNA Rchitect web app that we have hosted or to a version they themselves have deployed. Using DNA Rchitect, the uploaded data allows the user to visualize different interactions of their sample, perform simple network analyses, while also offering visualization of other genomic data types. The user can then download their results for additional network functionality offered in network based programs such as Cytoscape. AVAILABILITY AND IMPLEMENTATION: DNA Rchitect is freely available both as a web application written primarily in R available at http://shiny.immgen.org/DNARchitect/ and as an open source released under an MIT license at: https://github.com/alosdiallo/DNA_Rchitect.
Authors: Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker Journal: Genome Res Date: 2003-11 Impact factor: 9.043
Authors: Adrian L Sanborn; Suhas S P Rao; Su-Chen Huang; Neva C Durand; Miriam H Huntley; Andrew I Jewett; Ivan D Bochkov; Dharmaraj Chinnappan; Ashok Cutkosky; Jian Li; Kristopher P Geeting; Andreas Gnirke; Alexandre Melnikov; Doug McKenna; Elena K Stamenova; Eric S Lander; Erez Lieberman Aiden Journal: Proc Natl Acad Sci U S A Date: 2015-10-23 Impact factor: 11.205
Authors: Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker Journal: Science Date: 2009-10-09 Impact factor: 47.728
Authors: Paul Martin; Amanda McGovern; Jonathan Massey; Stefan Schoenfelder; Kate Duffus; Annie Yarwood; Anne Barton; Jane Worthington; Peter Fraser; Stephen Eyre; Gisela Orozco Journal: PLoS One Date: 2016-11-18 Impact factor: 3.240
Authors: Paul Martin; Amanda McGovern; Gisela Orozco; Kate Duffus; Annie Yarwood; Stefan Schoenfelder; Nicholas J Cooper; Anne Barton; Chris Wallace; Peter Fraser; Jane Worthington; Steve Eyre Journal: Nat Commun Date: 2015-11-30 Impact factor: 14.919
Authors: Jurian Schuijers; John Colonnese Manteiga; Abraham Selby Weintraub; Daniel Sindt Day; Alicia Viridiana Zamudio; Denes Hnisz; Tong Ihn Lee; Richard Allen Young Journal: Cell Rep Date: 2018-04-10 Impact factor: 9.423