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CisGenome Browser: a flexible tool for genomic data visualization
2010
Bioinformatics
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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
2008
Nature Biotechnology
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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
2011
Genome Biology
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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
2011
Journal of Integrative Bioinformatics
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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
2011
Journal of Integrative Bioinformatics
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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
2011
Nucleic Acids Research
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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
2010
BMC Bioinformatics
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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
2013
Bioinformatics
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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
2014
BMC Research Notes
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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
2014
BMC Genomics
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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
2010
BMC Biology
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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
2010
Nature reviews genetics
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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
2012
Hereditary Genetics: Current Research
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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]
2017
bioRxiv
pre-print
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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
2017
BMC Bioinformatics
Preserved Fulltext
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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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