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Results: 1 to 20 of 181

1.

BigWig and BigBed: enabling browsing of large distributed datasets.

Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D.

Bioinformatics. 2010 Sep 1;26(17):2204-7. doi: 10.1093/bioinformatics/btq351. Epub 2010 Jul 17.

PMID:
20639541
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser.

Raney BJ, Dreszer TR, Barber GP, Clawson H, Fujita PA, Wang T, Nguyen N, Paten B, Zweig AS, Karolchik D, Kent WJ.

Bioinformatics. 2014 Apr 1;30(7):1003-5. doi: 10.1093/bioinformatics/btt637. Epub 2013 Nov 13.

PMID:
24227676
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

The UCSC genome browser and associated tools.

Kuhn RM, Haussler D, Kent WJ.

Brief Bioinform. 2013 Mar;14(2):144-61. doi: 10.1093/bib/bbs038. Epub 2012 Aug 20.

PMID:
22908213
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Navigating protected genomics data with UCSC Genome Browser in a Box.

Haeussler M, Raney BJ, Hinrichs AS, Clawson H, Zweig AS, Karolchik D, Casper J, Speir ML, Haussler D, Kent WJ.

Bioinformatics. 2014 Oct 27. pii: btu712. [Epub ahead of print]

PMID:
25348212
[PubMed - as supplied by publisher]
Free Article
5.

CWig: compressed representation of Wiggle/BedGraph format.

Huy Hoang D, Sung WK.

Bioinformatics. 2014 Sep 15;30(18):2543-50. doi: 10.1093/bioinformatics/btu330. Epub 2014 May 27.

PMID:
24867943
[PubMed - indexed for MEDLINE]
6.

BEDTools: a flexible suite of utilities for comparing genomic features.

Quinlan AR, Hall IM.

Bioinformatics. 2010 Mar 15;26(6):841-2. doi: 10.1093/bioinformatics/btq033. Epub 2010 Jan 28.

PMID:
20110278
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

The UCSC Genome Browser database: update 2011.

Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ.

Nucleic Acids Res. 2011 Jan;39(Database issue):D876-82. doi: 10.1093/nar/gkq963. Epub 2010 Oct 18.

PMID:
20959295
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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

Nicol JW, Helt GA, Blanchard SG Jr, Raja A, Loraine AE.

Bioinformatics. 2009 Oct 15;25(20):2730-1. doi: 10.1093/bioinformatics/btp472. Epub 2009 Aug 4.

PMID:
19654113
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

The UCSC Genome Browser Database.

Karolchik D, Baertsch R, Diekhans M, Furey TS, Hinrichs A, Lu YT, Roskin KM, Schwartz M, Sugnet CW, Thomas DJ, Weber RJ, Haussler D, Kent WJ; University of California Santa Cruz.

Nucleic Acids Res. 2003 Jan 1;31(1):51-4.

PMID:
12519945
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

UCSC genome browser tutorial.

Zweig AS, Karolchik D, Kuhn RM, Haussler D, Kent WJ.

Genomics. 2008 Aug;92(2):75-84. doi: 10.1016/j.ygeno.2008.02.003. Epub 2008 Jun 2. Review.

PMID:
18514479
[PubMed - indexed for MEDLINE]
Free Article
11.

The UCSC Genome Browser database: update 2010.

Rhead B, Karolchik D, Kuhn RM, Hinrichs AS, Zweig AS, Fujita PA, Diekhans M, Smith KE, Rosenbloom KR, Raney BJ, Pohl A, Pheasant M, Meyer LR, Learned K, Hsu F, Hillman-Jackson J, Harte RA, Giardine B, Dreszer TR, Clawson H, Barber GP, Haussler D, Kent WJ.

Nucleic Acids Res. 2010 Jan;38(Database issue):D613-9. doi: 10.1093/nar/gkp939. Epub 2009 Nov 11.

PMID:
19906737
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

The UCSC Genome Browser Database: update 2006.

Hinrichs AS, Karolchik D, Baertsch R, Barber GP, Bejerano G, Clawson H, Diekhans M, Furey TS, Harte RA, Hsu F, Hillman-Jackson J, Kuhn RM, Pedersen JS, Pohl A, Raney BJ, Rosenbloom KR, Siepel A, Smith KE, Sugnet CW, Sultan-Qurraie A, Thomas DJ, Trumbower H, Weber RJ, Weirauch M, Zweig AS, Haussler D, Kent WJ.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D590-8.

PMID:
16381938
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

ENCODE whole-genome data in the UCSC Genome Browser.

Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM, Karolchik D, Haussler D, Kent WJ.

Nucleic Acids Res. 2010 Jan;38(Database issue):D620-5. doi: 10.1093/nar/gkp961. Epub 2009 Nov 17.

PMID:
19920125
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Histogram-based DNA analysis for the visualization of chromosome, genome and species information.

Costa AM, Machado JT, Quelhas MD.

Bioinformatics. 2011 May 1;27(9):1207-14. doi: 10.1093/bioinformatics/btr131. Epub 2011 Mar 12.

PMID:
21398672
[PubMed - indexed for MEDLINE]
Free Article
15.

The UCSC Table Browser data retrieval tool.

Karolchik D, Hinrichs AS, Furey TS, Roskin KM, Sugnet CW, Haussler D, Kent WJ.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D493-6.

PMID:
14681465
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

ENCODE whole-genome data in the UCSC Genome Browser: update 2012.

Rosenbloom KR, Dreszer TR, Long JC, Malladi VS, Sloan CA, Raney BJ, Cline MS, Karolchik D, Barber GP, Clawson H, Diekhans M, Fujita PA, Goldman M, Gravell RC, Harte RA, Hinrichs AS, Kirkup VM, Kuhn RM, Learned K, Maddren M, Meyer LR, Pohl A, Rhead B, Wong MC, Zweig AS, Haussler D, Kent WJ.

Nucleic Acids Res. 2012 Jan;40(Database issue):D912-7. doi: 10.1093/nar/gkr1012. Epub 2011 Nov 9.

PMID:
22075998
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

bwtool: a tool for bigWig files.

Pohl A, Beato M.

Bioinformatics. 2014 Jun 1;30(11):1618-9. doi: 10.1093/bioinformatics/btu056. Epub 2014 Jan 30.

PMID:
24489365
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data.

Librado P, Rozas J.

Bioinformatics. 2009 Jun 1;25(11):1451-2. doi: 10.1093/bioinformatics/btp187. Epub 2009 Apr 3.

PMID:
19346325
[PubMed - indexed for MEDLINE]
Free Article
19.

DiProGB: the dinucleotide properties genome browser.

Friedel M, Nikolajewa S, Sühnel J, Wilhelm T.

Bioinformatics. 2009 Oct 1;25(19):2603-4. doi: 10.1093/bioinformatics/btp436. Epub 2009 Jul 15.

PMID:
19605418
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis.

Zerbino DR, Johnson N, Juettemann T, Wilder SP, Flicek P.

Bioinformatics. 2014 Apr 1;30(7):1008-9. doi: 10.1093/bioinformatics/btt737. Epub 2013 Dec 19.

PMID:
24363377
[PubMed - indexed for MEDLINE]
Free PMC Article

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