Phinch statistics

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Phinch specifications

Information


Unique identifier OMICS_18111
Name Phinch
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Holly Bik <>

Additional information


https://github.com/PitchInteractiveInc/Phinch; Blog: http://phinch.org/blog/

Information


Unique identifier OMICS_18111
Name Phinch
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Input data A metadata or a taxonomy/ontology information.
Input format BIOM
Operating system Unix/Linux
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 1.1.2
Stability Stable
Source code URL https://codeload.github.com/PitchInteractiveInc/Phinch/tar.gz/v1.1.2
Maintained Yes

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Documentation


Maintainer


  • person_outline Holly Bik <>

Additional information


https://github.com/PitchInteractiveInc/Phinch; Blog: http://phinch.org/blog/

Publication for Phinch

Phinch in publications

 (4)
PMCID: 5651271
PMID: 29093702
DOI: 10.3389/fmicb.2017.01997

[…] unite v7.0 database (abarenkov et al., ) and non-fungal otus were removed prior to downstream data processing. biom data from amptk pipeline was further analyzed using metacomet (wang et al., ) and phinch (bik and pitch interactive, ) to visually compare treatment and sites at each taxonomic level., all distance-matrix based community analyses were performed on a presence absence (binary) otu […]

PMCID: 5576765
PMID: 28861131
DOI: 10.1128/jmbe.v18i2.1284

[…] the bacterial communities that live on our bodies, even if they do not have access to sophisticated software or wet lab resources. students use an open-source, web browser-based bioinformatics tool, phinch.org, to visualize and interact with microbiome data from a citizen-science project that sampled over 270 belly buttons to investigate their microbial biodiversity (). while the students […]

PMCID: 4776111
PMID: 26935537
DOI: 10.1038/srep22541

[…] analysis of similarities (anosim) and similarity percentage (simper) were performed in r using vegan v2.0-8. community structure was analyzed in r with phyloseq and plotted with ggplot2 and phinch., dna from the sterivex samples collected from bottom seawater, u1382a, u1383c shallow, and u1383c deep was sheared to 175 bp using a covaris s-series sonicator. libraries were constructed […]

PMCID: 4378022
PMID: 25825673
DOI: 10.1186/s40168-015-0070-0

[…] used for similar previous meta-analyses [,]. sequences were analyzed by using both weighted and unweighted unifrac [], followed by principal coordinate analysis []. data were visualized using phinch. the phinch program provides an easy-to-use, browser-based, platform to visualize contingency tables along with their sample metadata (bik et al., manuscript in preparation, […]


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Phinch institution(s)
UC Davis Genome Center, University of California--Davis, CA, USA; School of Biosciences, The University of Birmingham, Edgbaston, Birmingham, USA; Pitch Interactive, Inc., Oakland, CA, USA

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