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Literature DB >> 20513664

CisGenome Browser: a flexible tool for genomic data visualization.

Hui Jiang¹, Fan Wang, Nigel P Dyer, Wing Hung Wong.

Abstract

SUMMARY: 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. It has features that are specifically designed for ultra high-throughput sequencing data visualization. AVAILABILITY: http://biogibbs.stanford.edu/ approximately jiangh/browser/

Mesh：

Year: 2010 PMID： 20513664 PMCID： PMC2894522 DOI： 10.1093/bioinformatics/btq286

Source DB: PubMed Journal: Bioinformatics ISSN： 1367-4803 Impact factor: 6.937

6 in total

1. The Sequence Alignment/Map format and SAMtools.

Authors: Heng Li; Bob Handsaker; Alec Wysoker; Tim Fennell; Jue Ruan; Nils Homer; Gabor Marth; Goncalo Abecasis; Richard Durbin
Journal: Bioinformatics Date: 2009-06-08 Impact factor: 6.937

2. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.

Authors: John W Nicol; Gregg A Helt; Steven G Blanchard; Archana Raja; Ann E Loraine
Journal: Bioinformatics Date: 2009-08-04 Impact factor: 6.937

3. Database resources of the National Center for Biotechnology Information.

Authors: David L Wheeler; Tanya Barrett; Dennis A Benson; Stephen H Bryant; Kathi Canese; Deanna M Church; Michael DiCuccio; Ron Edgar; Scott Federhen; Wolfgang Helmberg; David L Kenton; Oleg Khovayko; David J Lipman; Thomas L Madden; Donna R Maglott; James Ostell; Joan U Pontius; Kim D Pruitt; Gregory D Schuler; Lynn M Schriml; Edwin Sequeira; Steven T Sherry; Karl Sirotkin; Grigory Starchenko; Tugba O Suzek; Roman Tatusov; Tatiana A Tatusova; Lukas Wagner; Eugene Yaschenko
Journal: Nucleic Acids Res Date: 2005-01-01 Impact factor: 16.971

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

Authors: Hongkai Ji; Hui Jiang; Wenxiu Ma; David S Johnson; Richard M Myers; Wing H Wong
Journal: Nat Biotechnol Date: 2008-11-02 Impact factor: 54.908

5. The UCSC Genome Browser Database: 2008 update.

Authors: D Karolchik; R M Kuhn; R Baertsch; G P Barber; H Clawson; M Diekhans; B Giardine; R A Harte; A S Hinrichs; F Hsu; K M Kober; W Miller; J S Pedersen; A Pohl; B J Raney; B Rhead; K R Rosenbloom; K E Smith; M Stanke; A Thakkapallayil; H Trumbower; T Wang; A S Zweig; D Haussler; W J Kent
Journal: Nucleic Acids Res Date: 2007-12-17 Impact factor: 16.971

6. Ensembl 2008.

Authors: P Flicek; B L Aken; K Beal; B Ballester; M Caccamo; Y Chen; L Clarke; G Coates; F Cunningham; T Cutts; T Down; S C Dyer; T Eyre; S Fitzgerald; J Fernandez-Banet; S Gräf; S Haider; M Hammond; R Holland; K L Howe; K Howe; N Johnson; A Jenkinson; A Kähäri; D Keefe; F Kokocinski; E Kulesha; D Lawson; I Longden; K Megy; P Meidl; B Overduin; A Parker; B Pritchard; A Prlic; S Rice; D Rios; M Schuster; I Sealy; G Slater; D Smedley; G Spudich; S Trevanion; A J Vilella; J Vogel; S White; M Wood; E Birney; T Cox; V Curwen; R Durbin; X M Fernandez-Suarez; J Herrero; T J P Hubbard; A Kasprzyk; G Proctor; J Smith; A Ureta-Vidal; S Searle
Journal: Nucleic Acids Res Date: 2007-11-13 Impact factor: 16.971

6 in total

22 in total

1. Neonatal thymectomy reveals differentiation and plasticity within human naive T cells.

Authors: Theo van den Broek; Eveline M Delemarre; Willemijn J M Janssen; Rutger A J Nievelstein; Jasper C Broen; Kiki Tesselaar; Jose A M Borghans; Edward E S Nieuwenhuis; Berent J Prakken; Michal Mokry; Nicolaas J G Jansen; Femke van Wijk
Journal: J Clin Invest Date: 2016-02-22 Impact factor: 14.808

10. ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor.

Authors: Jing Qin; Mulin Jun Li; Panwen Wang; Michael Q Zhang; Junwen Wang
Journal: Nucleic Acids Res Date: 2011-05-17 Impact factor: 16.971

CisGenome Browser: a flexible tool for genomic data visualization.

1. The Sequence Alignment/Map format and SAMtools.

2. The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets.

3. Database resources of the National Center for Biotechnology Information.

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

5. The UCSC Genome Browser Database: 2008 update.

6. Ensembl 2008.

1. Neonatal thymectomy reveals differentiation and plasticity within human naive T cells.

2. An interactive environment for agile analysis and visualization of ChIP-sequencing data.

3. AP-1 family members act with Sox9 to promote chondrocyte hypertrophy.

4. A penalized likelihood approach for robust estimation of isoform expression.

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

6. The MADS-domain factor AGAMOUS-Like18 promotes somatic embryogenesis.

7. Six2 and Wnt regulate self-renewal and commitment of nephron progenitors through shared gene regulatory networks.

8. Statistical Modeling of RNA-Seq Data.

9. Histone methyltransferase MLL3 contributes to genome-scale circadian transcription.

10. ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor.