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Open Source Science

https://github.com/alisaei/phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

https://github.com/alisaei/phyloseq

Science Score: 23.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: arxiv.org, plos.org
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    Academic email domains
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.4%) to scientific vocabulary
Last synced: 9 months ago · JSON representation

Repository

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

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Fork of joey711/phyloseq
Created over 7 years ago · Last pushed almost 8 years ago

https://github.com/AliSaei/phyloseq/blob/master/ 



# [phyloseq](http://joey711.github.com/phyloseq/)

[![Travis-CI Build Status](https://travis-ci.org/joey711/phyloseq.svg?branch=master)](https://travis-ci.org/joey711/phyloseq)

## Article on Improved Microbiome Analysis

McMurdie and Holmes (2014)
[Waste Not, Want Not: Why Rarefying Microbiome Data is Statistically Inadmissible](http://dx.plos.org/10.1371/journal.pcbi.1003531)
*PLoS Computational Biology*
10(4): e1003531

Presubmission versions ahead of acceptance (2013):
[PDF version 2](http://arxiv.org/pdf/1310.0424v2.pdf),
[PDF version 1](http://arxiv.org/pdf/1310.0424v1.pdf)


## Peer-reviewed articles about phyloseq

McMurdie and Holmes (2014) [Shiny-phyloseq: Web Application for Interactive Microbiome Analysis with Provenance Tracking](http://bioinformatics.oxfordjournals.org/content/early/2014/10/02/bioinformatics.btu616).
*Bioinformatics (Oxford, England)*
31(2), 282283.

McMurdie and Holmes (2013)
[phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data](http://dx.plos.org/10.1371/journal.pone.0061217)
*PLoS ONE* 
8(4):e61217

## Other resources

The phyloseq project also has a number of supporting online resources,
including (but probably not limited to)

### [the phyloseq home page](http://joey711.github.com/phyloseq/)

### [the phyloseq FAQ](https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-FAQ.html)
I recommend checking this page, and the issues tracker,
before posting new issues.

### [Bioconductor stable release](http://bioconductor.org/packages/release/bioc/html/phyloseq.html).

### [the phyloseq Issue Tracker](https://github.com/joey711/phyloseq/issues)
This is the recommended location to post

(1) feature requests
(2) bug reports
(3) theoretical considerations
(4) other issues, feedback
(5) ask for help

Search previous posts,
and check [the phyloseq FAQ](https://www.bioconductor.org/packages/release/bioc/vignettes/phyloseq/inst/doc/phyloseq-FAQ.html)
before posting a new issue.

Owner

  • Name: Ali
  • Login: AliSaei
  • Kind: user

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