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Items: 1 to 20 of 72

1.

AXIOME: automated exploration of microbial diversity.

Lynch MDj, Masella AP, Hall MW, Bartram AK, Neufeld JD.

Gigascience. 2013 Mar 13;2(1):3. doi: 10.1186/2047-217X-2-3.

2.

SSUnique: Detecting Sequence Novelty in Microbiome Surveys.

Lynch MD, Neufeld JD.

mSystems. 2016 Dec 20;1(6). pii: e00133-16. doi: 10.1128/mSystems.00133-16. eCollection 2016 Nov-Dec.

3.

mcaGUI: microbial community analysis R-Graphical User Interface (GUI).

Copeland WK, Krishnan V, Beck D, Settles M, Foster JA, Cho KC, Day M, Hickey R, Schütte UM, Zhou X, Williams CJ, Forney LJ, Abdo Z.

Bioinformatics. 2012 Aug 15;28(16):2198-9. doi: 10.1093/bioinformatics/bts338. Epub 2012 Jun 12.

4.

RevEcoR: an R package for the reverse ecology analysis of microbiomes.

Cao Y, Wang Y, Zheng X, Li F, Bo X.

BMC Bioinformatics. 2016 Jul 29;17(1):294. doi: 10.1186/s12859-016-1088-4.

5.

Seed: a user-friendly tool for exploring and visualizing microbial community data.

Beck D, Dennis C, Foster JA.

Bioinformatics. 2015 Feb 15;31(4):602-3. doi: 10.1093/bioinformatics/btu693. Epub 2014 Oct 20.

6.
7.

Analysis of 16S rRNA Gene Amplicon Sequences Using the QIIME Software Package.

Lawley B, Tannock GW.

Methods Mol Biol. 2017;1537:153-163.

PMID:
27924593
8.

Visualizing Patterns of Marine Eukaryotic Diversity from Metabarcoding Data Using QIIME.

Leray M, Knowlton N.

Methods Mol Biol. 2016;1452:219-35. doi: 10.1007/978-1-4939-3774-5_15.

PMID:
27460381
9.

iFlow: A Graphical User Interface for Flow Cytometry Tools in Bioconductor.

Lee K, Hahne F, Sarkar D, Gentleman R.

Adv Bioinformatics. 2009:103839. doi: 10.1155/2009/103839. Epub 2009 Nov 12.

10.

JAGUC--a software package for environmental diversity analyses.

Nebel ME, Wild S, Holzhauser M, Hüttenberger L, Reitzig R, Sperber M, Stoeck T.

J Bioinform Comput Biol. 2011 Dec;9(6):749-73.

PMID:
22084012
11.

Introducing W.A.T.E.R.S.: a workflow for the alignment, taxonomy, and ecology of ribosomal sequences.

Hartman AL, Riddle S, McPhillips T, Ludäscher B, Eisen JA.

BMC Bioinformatics. 2010 Jun 12;11:317. doi: 10.1186/1471-2105-11-317.

12.

Bioinformatic Suggestions on MiSeq-Based Microbial Community Analysis.

Unno T.

J Microbiol Biotechnol. 2015 Jun;25(6):765-70.

13.

Explicet: graphical user interface software for metadata-driven management, analysis and visualization of microbiome data.

Robertson CE, Harris JK, Wagner BD, Granger D, Browne K, Tatem B, Feazel LM, Park K, Pace NR, Frank DN.

Bioinformatics. 2013 Dec 1;29(23):3100-1. doi: 10.1093/bioinformatics/btt526. Epub 2013 Sep 10.

14.

bioNMF: a web-based tool for nonnegative matrix factorization in biology.

Mejía-Roa E, Carmona-Saez P, Nogales R, Vicente C, Vázquez M, Yang XY, García C, Tirado F, Pascual-Montano A.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W523-8. doi: 10.1093/nar/gkn335. Epub 2008 May 30.

15.

Molecular ecological network analyses.

Deng Y, Jiang YH, Yang Y, He Z, Luo F, Zhou J.

BMC Bioinformatics. 2012 May 30;13:113. doi: 10.1186/1471-2105-13-113.

16.

PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data.

Anslan S, Bahram M, Hiiesalu I, Tedersoo L.

Mol Ecol Resour. 2017 May 25. doi: 10.1111/1755-0998.12692. [Epub ahead of print]

PMID:
28544559
17.

Sushi.R: flexible, quantitative and integrative genomic visualizations for publication-quality multi-panel figures.

Phanstiel DH, Boyle AP, Araya CL, Snyder MP.

Bioinformatics. 2014 Oct;30(19):2808-10. doi: 10.1093/bioinformatics/btu379. Epub 2014 Jun 5.

18.

Chipster: user-friendly analysis software for microarray and other high-throughput data.

Kallio MA, Tuimala JT, Hupponen T, Klemelä P, Gentile M, Scheinin I, Koski M, Käki J, Korpelainen EI.

BMC Genomics. 2011 Oct 14;12:507. doi: 10.1186/1471-2164-12-507.

19.

The missing graphical user interface for genomics.

Schatz MC.

Genome Biol. 2010;11(8):128. doi: 10.1186/gb-2010-11-8-128. Epub 2010 Aug 25.

20.

Phylogenetic molecular ecological network of soil microbial communities in response to elevated CO2.

Zhou J, Deng Y, Luo F, He Z, Yang Y.

MBio. 2011 Jul 26;2(4). pii: e00122-11. doi: 10.1128/mBio.00122-11. Print 2011.

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