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Items: 1 to 20 of 68

1.

ACT: aggregation and correlation toolbox for analyses of genome tracks.

Jee J, Rozowsky J, Yip KY, Lochovsky L, Bjornson R, Zhong G, Zhang Z, Fu Y, Wang J, Weng Z, Gerstein M.

Bioinformatics. 2011 Apr 15;27(8):1152-4. doi: 10.1093/bioinformatics/btr092. Epub 2011 Feb 23.

2.

GenomicTools: a computational platform for developing high-throughput analytics in genomics.

Tsirigos A, Haiminen N, Bilal E, Utro F.

Bioinformatics. 2012 Jan 15;28(2):282-3. doi: 10.1093/bioinformatics/btr646. Epub 2011 Nov 22.

PMID:
22113082
3.

The Genomic HyperBrowser: an analysis web server for genome-scale data.

Sandve GK, Gundersen S, Johansen M, Glad IK, Gunathasan K, Holden L, Holden M, Liestøl K, Nygård S, Nygaard V, Paulsen J, Rydbeck H, Trengereid K, Clancy T, Drabløs F, Ferkingstad E, Kalas M, Lien T, Rye MB, Frigessi A, Hovig E.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W133-41. doi: 10.1093/nar/gkt342. Epub 2013 Apr 30.

4.

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data.

Jombart T, Ahmed I.

Bioinformatics. 2011 Nov 1;27(21):3070-1. doi: 10.1093/bioinformatics/btr521. Epub 2011 Sep 16.

5.

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.

Habegger L, Sboner A, Gianoulis TA, Rozowsky J, Agarwal A, Snyder M, Gerstein M.

Bioinformatics. 2011 Jan 15;27(2):281-3. doi: 10.1093/bioinformatics/btq643. Epub 2010 Dec 5.

6.

Genome Maps, a new generation genome browser.

Medina I, Salavert F, Sanchez R, de Maria A, Alonso R, Escobar P, Bleda M, Dopazo J.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W41-6. doi: 10.1093/nar/gkt530. Epub 2013 Jun 8.

7.

GenPlay, a multipurpose genome analyzer and browser.

Lajugie J, Bouhassira EE.

Bioinformatics. 2011 Jul 15;27(14):1889-93. doi: 10.1093/bioinformatics/btr309. Epub 2011 May 19.

PMID:
21596789
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.

9.

GPAT: retrieval of genomic annotation from large genomic position datasets.

Krebs A, Frontini M, Tora L.

BMC Bioinformatics. 2008 Dec 15;9:533. doi: 10.1186/1471-2105-9-533.

10.

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.

Lefrançois P, Euskirchen GM, Auerbach RK, Rozowsky J, Gibson T, Yellman CM, Gerstein M, Snyder M.

BMC Genomics. 2009 Jan 21;10:37. doi: 10.1186/1471-2164-10-37.

11.

TRES: Identification of Discriminatory and Informative SNPs from Population Genomic Data.

Kavakiotis I, Triantafyllidis A, Ntelidou D, Alexandri P, Megens HJ, Crooijmans RP, Groenen MA, Tsoumakas G, Vlahavas I.

J Hered. 2015 Sep-Oct;106(5):672-6. doi: 10.1093/jhered/esv044. Epub 2015 Jul 2.

PMID:
26137847
12.

GMD: measuring the distance between histograms with applications on high-throughput sequencing reads.

Zhao X, Sandelin A.

Bioinformatics. 2012 Apr 15;28(8):1164-5. doi: 10.1093/bioinformatics/bts087. Epub 2012 Feb 17.

PMID:
22345619
13.

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.

14.

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

Alawi M, Kurtz S, Beckstette M.

J Integr Bioinform. 2011 Jun 21;8(2):155. doi: 10.2390/biecoll-jib-2011-155.

PMID:
21690655
15.

rtracklayer: an R package for interfacing with genome browsers.

Lawrence M, Gentleman R, Carey V.

Bioinformatics. 2009 Jul 15;25(14):1841-2. doi: 10.1093/bioinformatics/btp328. Epub 2009 May 25.

16.

PeakAnalyzer: genome-wide annotation of chromatin binding and modification loci.

Salmon-Divon M, Dvinge H, Tammoja K, Bertone P.

BMC Bioinformatics. 2010 Aug 6;11:415. doi: 10.1186/1471-2105-11-415.

17.

synbreed: a framework for the analysis of genomic prediction data using R.

Wimmer V, Albrecht T, Auinger HJ, Schön CC.

Bioinformatics. 2012 Aug 1;28(15):2086-7. doi: 10.1093/bioinformatics/bts335. Epub 2012 Jun 10.

PMID:
22689388
18.

ChromoZoom: a flexible, fluid, web-based genome browser.

Pak TR, Roth FP.

Bioinformatics. 2013 Feb 1;29(3):384-6. doi: 10.1093/bioinformatics/bts695. Epub 2012 Dec 6.

19.

Identifying elemental genomic track types and representing them uniformly.

Gundersen S, Kalaš M, Abul O, Frigessi A, Hovig E, Sandve GK.

BMC Bioinformatics. 2011 Dec 30;12:494. doi: 10.1186/1471-2105-12-494.

20.

Mapping personal functional data to personal genomes.

Rivas-Astroza M, Xie D, Cao X, Zhong S.

Bioinformatics. 2011 Dec 15;27(24):3427-9. doi: 10.1093/bioinformatics/btr578. Epub 2011 Oct 17.

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