OTUbase: an R infrastructure package for operational taxonomic unit data

被引：11
作者：
Beck, Daniel [1 ]
Settles, Matt [1 ]
Foster, James A. [1 ]
机构：
[1] Univ Idaho, Dept Biol Sci, Moscow, ID 83843 USA
来源：
BIOINFORMATICS | 2011年 / 27卷 / 12期
基金：
美国国家卫生研究院;
关键词：
DIVERSITY;
D O I：
10.1093/bioinformatics/btr196
中图分类号：
Q5 [生物化学];
学科分类号：
071010 ; 081704 ;
摘要：
OTUbase is an R package designed to facilitate the analysis of operational taxonomic unit (OTU) data and sequence classification (taxonomic) data. Currently there are programs that will cluster sequence data into OTUs and/or classify sequence data into known taxonomies. However, there is a need for software that can take the summarized output of these programs and organize it into easily accessed and manipulated formats. OTUbase provides this structure and organization within R, to allow researchers to easily manipulate the data with the rich library of R packages currently available for additional analysis.
引用
收藏
页码：1700 / 1701
页数：2
相关论文
共 8 条
  • [1] QIIME allows analysis of high-throughput community sequencing data
    Caporaso, J. Gregory
    Kuczynski, Justin
    Stombaugh, Jesse
    Bittinger, Kyle
    Bushman, Frederic D.
    Costello, Elizabeth K.
    Fierer, Noah
    Pena, Antonio Gonzalez
    Goodrich, Julia K.
    Gordon, Jeffrey I.
    Huttley, Gavin A.
    Kelley, Scott T.
    Knights, Dan
    Koenig, Jeremy E.
    Ley, Ruth E.
    Lozupone, Catherine A.
    McDonald, Daniel
    Muegge, Brian D.
    Pirrung, Meg
    Reeder, Jens
    Sevinsky, Joel R.
    Tumbaugh, Peter J.
    Walters, William A.
    Widmann, Jeremy
    Yatsunenko, Tanya
    Zaneveld, Jesse
    Knight, Rob
    [J]. NATURE METHODS, 2010, 7 (05) : 335 - 336
  • [2] The Ribosomal Database Project: improved alignments and new tools for rRNA analysis
    Cole, J. R.
    Wang, Q.
    Cardenas, E.
    Fish, J.
    Chai, B.
    Farris, R. J.
    Kulam-Syed-Mohideen, A. S.
    McGarrell, D. M.
    Marsh, T.
    Garrity, G. M.
    Tiedje, J. M.
    [J]. NUCLEIC ACIDS RESEARCH, 2009, 37 : D141 - D145
  • [3] PANGEA: pipeline for analysis of next generation amplicons
    Giongo, Adriana
    Crabb, David B.
    Davis-Richardson, Austin G.
    Chauliac, Diane
    Mobberley, Jennifer M.
    Gano, Kelsey A.
    Mukherjee, Nabanita
    Casella, George
    Roesch, Luiz F. W.
    Walts, Brandon
    Riva, Alberto
    King, Gary
    Triplett, Eric W.
    [J]. ISME JOURNAL, 2010, 4 (07) : 852 - 861
  • [4] Hugenholtz P, 2002, GENOME BIOL, V3
  • [5] Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates
    Kunin, Victor
    Engelbrektson, Anna
    Ochman, Howard
    Hugenholtz, Philip
    [J]. ENVIRONMENTAL MICROBIOLOGY, 2010, 12 (01) : 118 - 123
  • [6] Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
    Schloss, Patrick D.
    Westcott, Sarah L.
    Ryabin, Thomas
    Hall, Justine R.
    Hartmann, Martin
    Hollister, Emily B.
    Lesniewski, Ryan A.
    Oakley, Brian B.
    Parks, Donovan H.
    Robinson, Courtney J.
    Sahl, Jason W.
    Stres, Blaz
    Thallinger, Gerhard G.
    Van Horn, David J.
    Weber, Carolyn F.
    [J]. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2009, 75 (23) : 7537 - 7541
  • [7] Microbial diversity in the deep sea and the underexplored "rare biosphere"
    Sogin, Mitchell L.
    Morrison, Hilary G.
    Huber, Julie A.
    Mark Welch, David
    Huse, Susan M.
    Neal, Phillip R.
    Arrieta, Jesus M.
    Herndl, Gerhard J.
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (32) : 12115 - 12120
  • [8] Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy
    Wang, Qiong
    Garrity, George M.
    Tiedje, James M.
    Cole, James R.
    [J]. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2007, 73 (16) : 5261 - 5267
1