Package: MGnifyR 1.9.0

Tuomas Borman

MGnifyR: R interface to EBI MGnify metagenomics resource

Utility package to facilitate integration and analysis of EBI MGnify data in R. The package can be used to import microbial data for instance into TreeSummarizedExperiment (TreeSE). In TreeSE format, the data is directly compatible with miaverse framework.

Authors:Tuomas Borman [aut, cre], Ben Allen [aut], Leo Lahti [aut]

MGnifyR_1.9.0.tar.gz
MGnifyR_1.9.0.zip(r-4.7-any)MGnifyR_1.9.0.zip(r-4.6-any)MGnifyR_1.9.0.zip(r-4.5-any)
MGnifyR_1.9.0.tgz(r-4.6-any)MGnifyR_1.9.0.tgz(r-4.5-any)
MGnifyR_1.9.0.tar.gz(r-4.7-any)MGnifyR_1.9.0.tar.gz(r-4.6-any)
MGnifyR_1.9.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
MGnifyR/json (API)

# Install 'MGnifyR' in R:
install.packages('MGnifyR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ebi-metagenomics/mgnifyr/issues

On BioConductor:MGnifyR-1.9.0(bioc 3.24)MGnifyR-1.8.0(bioc 3.23)

infrastructuredataimportmetagenomicsmicrobiomemicrobiomedata

7.55 score 23 stars 43 scripts 352 downloads 32 exports 123 dependencies

Last updated from:8023712cff. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

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bioc-checksERROR211
linux-develNOTE962
source / vignettesOK351
linux-releaseNOTE975
macos-releaseNOTE806
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windows-develNOTE812
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wasm-releaseOK203

Exports:authTokauthTok<-cacheDircacheDir<-clearCacheclearCache<-databaseUrldatabaseUrl<-doQuerygetDatagetFilegetMetadatagetResultmgnify_analyses_from_samplesmgnify_analyses_from_studiesmgnify_clientmgnify_downloadmgnify_get_analyses_metadatamgnify_get_analyses_phyloseqmgnify_get_analyses_resultsmgnify_get_download_urlsmgnify_querymgnify_retrieve_jsonMgnifyClientsearchAnalysissearchFileshowWarningsshowWarnings<-useCacheuseCache<-verboseverbose<-

Dependencies:abindapeaskpassassortheadbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocNeighborsBiocParallelBiocSingularBiostringsblustercliclustercodetoolscpp11crayoncurlDBIDECIPHERdecontamDelayedArrayDelayedMatrixStatsdigestDirichletMultinomialdplyrdqrngecodivefarverFNNformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggbeeswarmggplot2ggrepelgluegridExtragtablehttrigraphIRangesirlbaisobandjsonlitelabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmiamimeMultiAssayExperimentnlmeopensslpermutepheatmappillarpkgconfigplyrpurrrR6rappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressRdpackreshape2rlangRSpectrarsvdRtsneS4ArraysS4VectorsS7ScaledMatrixscalesscaterscuttleSeqinfoSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsystibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimenttriebeardurltoolsutf8uwotvctrsveganviporviridisviridisLitewithrXVectoryulab.utils

Metagenomics bioinformatics at MGnify
Introduction | Load packages | Data import | Preprocessing | Alpha diversity | Beta diversity | Differential abundance analysis (DAA) | Session info
Rendered fromMGnify_course.Rmdusingknitr::rmarkdown

Last update: 2024-09-26
Started: 2024-09-25

MGnifyR
Introduction | Installation | Load MGnifyR package | Create a client | Functions for fetching the data | Search data | Find relevent analyses accessions | Fetch metadata | Fetch microbiome data | Fetch raw files | Fetch sequence files
Rendered fromMGnifyR.Rmdusingknitr::rmarkdown

Last update: 2024-09-25
Started: 2020-09-11

MGnifyR, extended vignette
Introduction | Installation | Load MGnifyR package | Create a client | Functions for fetching the data | Search data | Find relevent analyses accessions | Fetch metadata | Fetch microbiome data | Amplicon sequencing | Metagenomics | Fetch raw files | Fetch sequence files
Rendered fromMGnifyR_long.Rmdusingknitr::rmarkdown

Last update: 2024-09-25
Started: 2023-10-30

Readme and manuals

Help Manual

Help pageTopics
'MGnifyR' Package.MGnifyR-package MGnifyR
MgnifyClient accessors and mutatorsauthTok authTok,MgnifyClient-method authTok<- authTok<-,MgnifyClient-method cacheDir cacheDir,MgnifyClient-method cacheDir<- cacheDir<-,MgnifyClient-method clearCache clearCache,MgnifyClient-method clearCache<- clearCache<-,MgnifyClient-method databaseUrl databaseUrl,MgnifyClient-method databaseUrl<- databaseUrl<-,MgnifyClient-method MgnifyClient-accessors showWarnings showWarnings,MgnifyClient-method showWarnings<- showWarnings<-,MgnifyClient-method useCache useCache,MgnifyClient-method useCache<- useCache<-,MgnifyClient-method verbose verbose,MgnifyClient-method verbose<- verbose<-,MgnifyClient-method
These functions will be deprecated. Please use other functions instead.deprecate mgnify_analyses_from_samples mgnify_analyses_from_studies mgnify_client mgnify_download mgnify_get_analyses_metadata mgnify_get_analyses_phyloseq mgnify_get_analyses_results mgnify_get_download_urls mgnify_query mgnify_retrieve_json
Search MGnify database for studies, samples, runs, analyses, biomes, assemblies, and genomes.doQuery doQuery,MgnifyClient-method
Versatile function to retrieve raw resultsgetData getData,MgnifyClient-method
Download any MGnify files, also including processed reads and identified protein sequencesgetFile getFile,MgnifyClient-method searchFile searchFile,MgnifyClient-method
Get all study, sample and analysis metadata for the supplied analysis accessionsgetMetadata getMetadata,MgnifyClient-method
Get microbial and/or functional profiling data for a list of accessionsgetResult getResult,MgnifyClient-method
Constructor for creating a MgnifyClient object to allow the access to MGnify database.MgnifyClient MgnifyClient-class
Look up analysis accession IDs for one or more study or sample accessionssearchAnalysis searchAnalysis,MgnifyClient-method