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MGnifyR

R package for searching, downloading and analysis of EBI MGnify metagenomics data

https://github.com/ebi-metagenomics/mgnifyr

Science Score: 26.0%

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    CITATION.cff file
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    Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

R package for searching, downloading and analysis of EBI MGnify metagenomics data

Basic Info
Statistics
  • Stars: 22
  • Watchers: 5
  • Forks: 10
  • Open Issues: 5
  • Releases: 0
Created over 6 years ago · Last pushed about 1 year ago
Metadata Files
Readme Changelog License

README.md

MGnifyR

An R package for searching and retrieving data from the EBI Metagenomics resource. In most cases, MGnifyR interacts directly with the JSONAPI, rather than relying on downloading analyses outputs as TSV files. Thus it is more general - allowing for example the intuitive combining of multiple studies and analyses into a single workflow, but is in some cases slower than the afformentioned direct access. Local caching of results on disk is implemented to help counter some of the overheads, but data downloads can be slow - particularly for functional annotation retrieval.

MGnifyR package is part of miaverse microbiome analysis ecosystem enabling usage of mia and other miaverse packages.

This research has received funding from the Horizon 2020 Programme of the European Union within the FindingPheno project under grant agreement No 952914. FindingPheno, an EU-funded project, is dedicated to developing computational tools and methodologies for the integration and analysis of multi-omics data. Its primary objective is to deepen our understanding of the interactions between hosts and their microbiomes. You can find more information on FindingPheno website.

Installation

Bioc-release

``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("MGnifyR") ```

Bioc-devel

``` if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

The following initializes usage of Bioc devel

BiocManager::install(version='devel')

BiocManager::install("MGnifyR") ```

GitHub

remotes::install_github("EBI-Metagenomics/MGnifyR")

Basic usage

For more detailed instructions read the associated function help and vignette (vignette("MGNifyR"))

``` library(MGnifyR)

Set up the MGnify client instance

mg <- MgnifyClient(useCache = TRUE, cacheDir = '/tmp/MGnify_cache')

Retrieve the list of analyses associated with a study

accession_list <- searchAnalysis(mg, "studies", "MGYS00005058")

Download all associated study/sample and analysis metadata

metadataframe <- getMetadata(mg, accessionlist)

Convert analyses outputs to a single MultiAssayExperiment object

mae <- getResult(mg, metadataframe$analysisaccession) mae ```

Owner

  • Name: MGnify
  • Login: EBI-Metagenomics
  • Kind: organization
  • Email: metagenomics-help@ebi.ac.uk
  • Location: Genome Campus, UK

MGnify (formerly known as EBImetagenomics) is a free resource for the assembly, analysis, archiving and browsing all types of microbiome derived sequence data

GitHub Events

Total
  • Issues event: 1
  • Watch event: 2
  • Delete event: 3
  • Issue comment event: 1
  • Push event: 8
  • Pull request event: 5
  • Fork event: 1
  • Create event: 4
Last Year
  • Issues event: 1
  • Watch event: 2
  • Delete event: 3
  • Issue comment event: 1
  • Push event: 8
  • Pull request event: 5
  • Fork event: 1
  • Create event: 4

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 18
  • Total pull requests: 34
  • Average time to close issues: 10 months
  • Average time to close pull requests: 6 days
  • Total issue authors: 13
  • Total pull request authors: 4
  • Average comments per issue: 1.94
  • Average comments per pull request: 0.41
  • Merged pull requests: 24
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 6
  • Average time to close issues: N/A
  • Average time to close pull requests: 1 day
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 0.83
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • antagomir (6)
  • TuomasBorman (2)
  • vgopikaa (1)
  • Cal-Thoma (1)
  • artur-sannikov (1)
  • rigormortis0 (1)
  • mweberr (1)
  • yazhinia (1)
  • Ales-ibt (1)
  • kafker (1)
  • s-meaden (1)
  • stitam (1)
  • alexschickele (1)
Pull Request Authors
  • TuomasBorman (46)
  • kgatel (5)
  • antagomir (2)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 4,430 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 3
  • Total maintainers: 1
bioconductor.org: MGnifyR

R interface to EBI MGnify metagenomics resource

  • Versions: 3
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 4,430 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 31.3%
Average: 42.7%
Downloads: 96.8%
Maintainers (1)
tuomas.v.borman@utu.fi
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • ape * imports
  • dplyr * imports
  • httr * imports
  • phyloseq * imports
  • plyr * imports
  • reshape2 * imports
  • urltools * imports
  • ggplot2 * suggests
  • knitr * suggests
  • rmarkdown * suggests
.github/workflows/rworkflows.yml actions
  • neurogenomics/rworkflows master composite