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gplots: Various R Programming Tools for Plotting Data
Gregory R. Warnes,Ben Bolker,L. Bonebakker,Robert Gentleman,Wha Liaw,T. Lumley,M Maechler,A. Magnusson,S. Moeller,Michael L. Schwartz,B Venables,Wolfgang Huber,Andy Liaw,R. Gregory,BB Warnes,Lodewijk Bonebakker,Robert Gentleman,Wolfgang Huber Andy Liaw,Thomas Lumley,Martin Maechler,Arni Magnusson,Steffen Moeller,Marc Schwartz,Bill Venables +23 more
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The article was published on 2015-01-01 and is currently open access. It has received 2632 citations till now.read more
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dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering
TL;DR: dendextend is an R package for creating and comparing visually appealing tree diagrams that provides utility functions for manipulating dendrogram objects as well as several advanced methods for comparing trees to one another (both statistically and visually).
Journal ArticleDOI
Practical innovations for high-throughput amplicon sequencing.
TL;DR: Improvements for sequencing 16S ribosomal RNA (rRNA) amplicons, a cornerstone technique in metagenomics, are described through unique tagging of template molecules before PCR, which substantially enriching microbial sequences without introducing bias.
Journal ArticleDOI
Comprehensive analysis of DNA methylation data with RnBeads
TL;DR: RnBeads is a software tool for large-scale analysis and interpretation of DNA methylation data, providing a user-friendly analysis workflow that yields detailed hypertext reports (http://rnbeads.mpi-inf.mpg).
Journal ArticleDOI
Root microbiota drive direct integration of phosphate stress and immunity
Gabriel Castrillo,Paulo José Pereira Lima Teixeira,Sur Herrera Paredes,Theresa F. Law,Laura de Lorenzo,Meghan E. Feltcher,Omri M. Finkel,Natalie W. Breakfield,Natalie W. Breakfield,Piotr A. Mieczkowski,Corbin D. Jones,Javier Paz-Ares,Jeffery L. Dangl +12 more
TL;DR: It is established that a genetic network controlling the phosphate stress response influences the structure of the root microbiome community, even under non-stress phosphate conditions, and that the master transcriptional regulators of phosphate Stress Response in Arabidopsis thaliana directly repress defence, consistent with plant prioritization of nutritional stress over defence.
Journal ArticleDOI
Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential
TL;DR: Genetic co-occurrences suggest that plasmids provide limited opportunities for biocides and metals to promote horizontal transfer of antibiotic resistance through co-selection, whereas ample possibilities exist for indirect selection via chromosomal BMRGs.
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