SitePainter specifications

Information


Unique identifier OMICS_14896
Name SitePainter
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input format SVG
Operating system Unix/Linux
Programming languages Javascript
Computer skills Medium
Version 1.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Antonio Gonzalez <>

Publication for SitePainter

SitePainter in publications

 (5)
PMCID: 4593236
PMID: 26437943
DOI: 10.1186/s40168-015-0114-5

[…] mouth), buccal mucosa (inside lining of the cheek), attached keratinized gingiva (gums covering the jaw bones), and palatine tonsils (sides at the back of the throat) (see additional file drawn by sitepainter []). sequences in this reference dataset included amplified regions of the v1–v3 and v3–v5 regions of the 16s rrna gene (additional file ), although there were more sequences associated […]

PMCID: 4352708
PMID: 25756611
DOI: 10.7554/eLife.04634.014

[…] product-moment correlation analyses were performed using r software. environmental surveillance heatmaps were generated based on taxonomic abundance tables generated in qiime and visualized using sitepainter 1.1 (). bacterial otu source-sink relationships were tested using sourcetracker () with 1000 burn-ins, 25 restarts, and rarefaction to 100 otus. source-tracking predictions used bacterial […]

PMCID: 3893169
PMID: 24454771
DOI: 10.1371/journal.pone.0084963

[…] srs013948, srs014475, srs014689, srs015062, srs019027, srs011086, srs011115, srs011140, srs011243, srs011306, srs011105. a schematic of the body sites sampled for this hmp study was produced by sitepainter visualization tool from knight, perrung, and gonzalez, university of colorado (http://www.hmpdacc/sp) and further modified from ., all reference genomes downloaded from jgi-img site […]

PMCID: 3686677
PMID: 23840468
DOI: 10.1371/journal.pone.0066437

[…] (surface type, sampling time) at a single sampling depth (400 otus)., environmental surveillance heatmaps were generated based on taxonomic abundance tables generated in qiime and visualized using sitepainter 1.1 ., in order to quantify net microbial biomass on winery surfaces throughout harvest season, quantitative pcr (qpcr) was used to enumerate total fungi and bacteria. surfaces […]

PMCID: 3553055
PMID: 23372757
DOI: 10.1371/journal.pone.0054703

[…] at the university of south carolina (environmental genomics core facility)., the barcoded pyrosequencing data was analyzed using the qiime database (www.microbio.me/qiime), qiime version 1.5.0-dev, sitepainter 1.1 and sourcetracker 0.9.4 ., as part of the qiime database processing pipeline, raw sequence data were split into samples by barcode, and low quality reads were filtered using […]


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SitePainter institution(s)
Department of Computer Science, Boulder, CO, USA; Department of Chemistry and Biochemistry, Boulder, CO, USA; Cooperative Institute for Research in Environmental Sciences, Boulder, CO, USA; Department of Ecology and Evolutionary Biology, University of Colorado at Boulder, Boulder, CO, USA; Howard Hughes Medical Institute, Boulder, CO, USA
SitePainter funding source(s)
Supported by National Institutes of Health (Grants 5-R01-HL0090480 & 3-R01-HG004872); the Crohns and Colitis Foundation of America (Grant WU-09-72/2905035N); The Bill & Melinda Gates Foundation (Grant WU-09-187/51678); and the Howard Hughes Medical Institute.

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