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CisGenome Browser: a flexible tool for genomic data visualization

H. Jiang, F. Wang, N. P. Dyer, W. H. Wong
2010 Bioinformatics  
We present an open source, platform independent tool, called CisGenome Browser, which can work together with any other data analysis program to serve as a flexible component for genomic data visualization  ...  It can also work by itself as a standalone genome browser. By working as a light-weight web server, CisGenome Browser is a convenient tool for data sharing between labs.  ...  ACKNOWLEDGEMENTS We thank Hongkai Ji and Wenxiu Ma for helpful advice. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btq286 pmid:20513664 pmcid:PMC2894522 fatcat:zjzr4fvx2vg5hdebgorw4ppkji

An integrated software system for analyzing ChIP-chip and ChIP-seq data

Hongkai Ji, Hui Jiang, Wenxiu Ma, David S Johnson, Richard M Myers, Wing H Wong
2008 Nature Biotechnology  
We present CisGenome, a software system for analyzing genome-wide chromatin immunoprecipitation (ChIP) data.  ...  We demonstrate the use of these tools by a comparative analysis of ChIP-chip and ChIP-seq data for the transcription factor NRSF/REST, a study of ChIP-seq analysis with or without a negative control sample  ...  Li for assistance with analyzing the ChIP-chip spike-in data.  ... 
doi:10.1038/nbt.1505 pmid:18978777 pmcid:PMC2596672 fatcat:jvro3fijl5e7jfy2lgkulc3ju4

Cistrome: an integrative platform for transcriptional regulation studies

Tao Liu, Jorge A Ortiz, Len Taing, Clifford A Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Swee S Wong, Jian Ma, Ying Lei, Utz J Pape, Michael Poidinger (+5 others)
2011 Genome Biology  
The increasing volume of ChIP-chip and ChIP-seq data being generated creates a challenge for standard, integrative and reproducible bioinformatics data analysis platforms.  ...  In addition to the standard Galaxy functions, Cistrome has 29 ChIP-chip-and ChIP-seq-specific tools in three major categories, from preliminary peak calling and correlation analyses to downstream genome  ...  We thank Lingling Shen, Wenbo Wang, Jacqueline Wentz, Josiah Altschuler and Kar Joon Chew for their contributions to the system implementation.  ... 
doi:10.1186/gb-2011-12-8-r83 pmid:21859476 pmcid:PMC3245621 fatcat:25h6ewu5jrax3kxcvchynlx24e

CASSys: an integrated software-system for the interactive analysis of ChIP-seq data

Malik Alawi, Stefan Kurtz, Michael Beckstette
2011 Journal of Integrative Bioinformatics  
The follow-up analyses allow for flexible user defined association of putative interaction sites with genes, visualization of their genomic context with an integrated genome browser, the detection of putative  ...  Chromatin-immunoprecipitation followed by massively parallel sequencing (ChIP-seq) has become the standard technique for analyzing these interactions on a genome-wide scale.  ...  Availability The web based part of the CASSys system for carrying out all interactive analyses is available at http://www.zbh.uni-hamburg.de/cassys.  ... 
doi:10.2390/biecoll-jib-2011-155 pmid:21690655 fatcat:biprq2v4kfg2zhmkqgndiwnnsm

CASSys: an integrated software-system for the interactive analysis of ChIP-seq data

Malik Alawi, Stefan Kurtz, Michael Beckstette
2011 Journal of Integrative Bioinformatics  
The follow-up analyses allow for flexible user defined association of putative interaction sites with genes, visualization of their genomic context with an integrated genome browser, the detection of putative  ...  Chromatin-immunoprecipitation followed bymassively parallel sequencing (ChIP-seq) has become the standard technique for analyzing these interactions on a genome-wide scale.  ...  Standard genome browsers, like the UCSC Genome Browser [17] , can be used to visualize binding sites within their genomic context.  ... 
doi:10.1515/jib-2011-155 fatcat:sr4v2wa33fan3e4y4plm4wbuea

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments

Jose M. Muiño, Marlous Hoogstraat, Roeland C. H. J. van Ham, Aalt D. J. van Dijk
2011 Nucleic Acids Research  
A QuickLoad server compatible with genome browsers is implemented for the storage and visualization of DNA-binding maps.  ...  Although several tools for the analysis of ChIP-seq data have been published recently, there is a growing demand, in particular in the plant research community, for computational resources with which such  ...  ACKNOWLEDGEMENTS We thank Jan van Haarst, Henri van de Geest and Bas te Lintel Hekkert for technical support and Dr Hailiang Mei for advice regarding GALAXY.  ... 
doi:10.1093/nar/gkr373 pmid:21609962 pmcid:PMC3125775 fatcat:4alzcmuc7ne27iwrt2l6mx3oby

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data

Lihua J Zhu, Claude Gazin, Nathan D Lawson, Hervé Pagès, Simon M Lin, David S Lapointe, Michael R Green
2010 BMC Bioinformatics  
Cruz (UCSC) Genome Browser as custom annotation tracks.  ...  and BSgenome, provides flexibility.  ...  and Ellen Kittler at the UMMS Deep Sequencing Core Facility for helpful discussion.  ... 
doi:10.1186/1471-2105-11-237 pmid:20459804 pmcid:PMC3098059 fatcat:q23nfrm6yzd43hi5226ds5c66e

STAR: an integrated solution to management and visualization of sequencing data

T. Wang, J. Liu, L. Shen, J. Tonti-Filippini, Y. Zhu, H. Jia, R. Lister, J. W. Whitaker, J. R. Ecker, A. H. Millar, B. Ren, W. Wang
2013 Bioinformatics  
On the client side, STAR leverages JavaScript, HTML5 Canvas and asynchronous communications to deliver a smoothly scrolling desktop-like graphical user interface with a suite of in-browser analysis tools  ...  Motivation: Easily visualization of complex data features is a necessary step to conduct studies on next-generation sequencing (NGS) data.  ...  INTRODUCTION Using genome-browser software to visualize sequence data is often a productive first step to take when tasked with extracting biological meaning from experimental results.  ... 
doi:10.1093/bioinformatics/btt558 pmid:24078702 pmcid:PMC3842760 fatcat:fcdzgjchejgabf4afmt66raxfq

jChIP: a graphical environment for exploratory ChIP-Seq data analysis

Krzysztof Chojnowski, Krzysztof Goryca, Tymon Rubel, Michal Mikula
2014 BMC Research Notes  
Conclusion: jChIP is a user-friendly GUI-based software for the analysis of ChIP-Seq data within context of known genomic features.  ...  Further, jChIP provides tools for discovering new and refining known genome-wide protein binding patterns.  ...  We thank Karol Bomsztyk for proofreading and comments on the manuscript.  ... 
doi:10.1186/1756-0500-7-676 pmid:25260876 pmcid:PMC4189168 fatcat:pkoax33dffd6tnm5qrxkoyzfke

ChIPseek, a web-based analysis tool for ChIP data

Ting-Wen Chen, Hsin-Pai Li, Chi-Ching Lee, Ruei-Chi Gan, Po-Jung Huang, Timothy H Wu, Cheng-Yang Lee, Yi-Feng Chang, Petrus Tang
2014 BMC Genomics  
The analysis tools built into ChIPseek, especially the ones for selecting and examine a subset of peaks from ChIP data, provides invaluable helps for exploring the high through-put data from either ChIP-seq  ...  Results: We present ChIPseek, a web-based tool for ChIP data analysis providing summary statistics in graphs and offering several commonly demanded analyses.  ...  Chi-Yang for his help on modifying the code of Ideogram Viewer.  ... 
doi:10.1186/1471-2164-15-539 pmid:24974934 pmcid:PMC4092222 fatcat:df52qjmbezd7penxljj7k5nvom

MochiView: versatile software for genome browsing and DNA motif analysis

Oliver R Homann, Alexander D Johnson
2010 BMC Biology  
We present MochiView, a platform-independent Java software that integrates browsing of genomic sequences, features, and data with DNA motif visualization and analysis in a visually-appealing and user-friendly  ...  As high-throughput technologies rapidly generate genome-scale data, it becomes increasingly important to visually integrate these data so that specific hypotheses can be formulated and tested.  ...  We are grateful to the creators of the UCSC genome browser for database design inspiration. We also thank L. Booth, C.  ... 
doi:10.1186/1741-7007-8-49 pmid:20409324 pmcid:PMC2867778 fatcat:vyve6h7ohndh3ivsevreocpkqm

Next-generation genomics: an integrative approach

R. David Hawkins, Gary C. Hon, Bing Ren
2010 Nature reviews genetics  
However, the large amount of information and diverse technology platforms pose multiple challenges for data access and processing.  ...  Epigenomics, transcriptomics, proteomics and genomics each provide an insightful, and yet one-dimensional, view of genome function; integrative analysis promises a unified, global view.  ...  R.D.H is supported by a postdoctoral fellowship from the American Cancer Society.  ... 
doi:10.1038/nrg2795 pmid:20531367 pmcid:PMC3321268 fatcat:cctzl35u6zbwhjpjj6x66gsku4

Advances in Bioinformatics Tools for High-Throughput Sequencing Data of DNA Methylation

Jianzhong Su
2012 Hereditary Genetics: Current Research  
Analysis of DNA methylation patterns on a genome-wide scale is essential to understanding the underlying mechanisms of DNA methylation.  ...  and resources for further analysis of DNA methylation.  ...  cam.ac.uk/software/ batman [23] CisGenome Browser A flexible tool for genomic data visualization http://biogibbs.stanford.  ... 
doi:10.4172/2161-1041.1000107 fatcat:5ixyr2ionnhgxhryo7hkihujza

C-State: An interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search [article]

Divya Tej Sowpati, Surabhi Srivastava, Jyotsna Dhawan, Rakesh K. Mishra
2017 bioRxiv   pre-print
Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data.  ...  C-State has an interactive, JavaScript-based graphical user interface and runs locally in modern web browsers that are pre-installed on all computers, thus eliminating the need for cumbersome data transfer  ...  Saketh Saxena is acknowledged for the C-State website design.  ... 
doi:10.1101/163634 fatcat:ixfa4224u5bklhu463vx2xdv34

C-State: an interactive web app for simultaneous multi-gene visualization and comparative epigenetic pattern search

Divya Tej Sowpati, Surabhi Srivastava, Jyotsna Dhawan, Rakesh K Mishra
2017 BMC Bioinformatics  
Comparative epigenomic analysis across multiple genes presents a bottleneck for bench biologists working with NGS data.  ...  C-State has an interactive, JavaScriptbased graphical user interface and runs locally in modern web browsers that are pre-installed on all computers, thus eliminating the need for cumbersome data transfer  ...  Saketh Saxena is acknowledged for the C-State website design.  ... 
doi:10.1186/s12859-017-1786-6 pmid:28929968 pmcid:PMC5606219 fatcat:rxueij2f75atfbjfk4rifh2kw4
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