https://github.com/vmikk/metagmisc

Miscellaneous functions for metagenomic analysis.
https://github.com/vmikk/metagmisc

metagenomic-analysis parser r

Last synced: about 1 month ago
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Miscellaneous functions for metagenomic analysis.

• Host: GitHub
• URL: https://github.com/vmikk/metagmisc
• Owner: vmikk
• License: mit
• Created: 2016-12-15T06:40:05.000Z (about 8 years ago)
• Default Branch: master
• Last Pushed: 2024-06-19T17:11:40.000Z (7 months ago)
• Last Synced: 2024-06-20T05:45:14.315Z (7 months ago)
• Topics: metagenomic-analysis, parser, r
• Language: R
• Size: 1.64 MB
• Stars: 44
• Watchers: 3
• Forks: 11
• Open Issues: 10
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# metagMisc 

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.571403.svg)](https://doi.org/10.5281/zenodo.571403)

[![CRAN_Status_Badge](http://www.r-pkg.org/badges/version/metagMisc)](https://cran.r-project.org/package=metagMisc)

[![Latest Github release](https://img.shields.io/github/release/vmikk/metagMisc.svg)](https://github.com/vmikk/metagMisc/releases/latest)

Miscellaneous functions for metagenomic analysis.  

metagMisc package contains miscellaneous functions for metabarcoding and metagenomic analysis, including data transformations, several parsers (for USERCH UC-format; BLAST, SINA and STAMPA outputs, etc.), taxonomy handlers (SILVA, QIIME, AMPTk), phyloseq-shortcuts (multiple rarefaction, phyloseq splitting and exporting), and DADA2-shortcuts (error rate estimation on the subset of data, export of denoised amplicons in fasta).  

The repository is currently in **ALPHA** state. Nothing is guaranteed and the material is subject to change without a notice (e.g., function names or arguments).  

# Getting started

Vignette is under construction.

# Package features

* Multiple rarefaction

* OTU abundance averaging following CoDa (Compositional Data Analysis) workflow

* Phylogenetic diversity estimation (including standardized effect sizes)

* Pairwise dissimilarity boxplots



* Prevalence plots (total OTU abundance vs OTU prevalence)



* Diversity profiles based on Hill numbers (with `entropart` package)



* Various data filtering options (e.g., extraction of the most abundant OTUs)



* Taxonomic resolution visualization



# Installation

```

devtools::install_github("vmikk/metagMisc")

```

## Dependencies

`source("http://bioconductor.org/biocLite.R")`

* phyloseq: `biocLite("phyloseq")`

* dada2: `biocLite("dada2")`

* ALDEx2: `biocLite("ALDEx2")`

* metagenomeSeq: `biocLite("metagenomeSeq")`

* DESeq2: `biocLite("DESeq2")`

* vegan: `install.packages("vegan")`

* ggplot2

* plyr

* openssl

# Acknowledgements

`metagMisc` stands on the shoulders of numerous R-packages (see Dependencies). In particular, it would not have happened without [phyloseq](https://github.com/joey711/phyloseq/) and [vegan](https://github.com/vegandevs/vegan/) packages. Please cite R and R packages when you use them for data analysis. 

The development of this software was supported by RFBR grants 16-04-01259 and 15-29-02765.