Package: MGnifyR 1.3.0

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_1.3.0.tar.gz
MGnifyR_1.3.0.zip(r-4.5)MGnifyR_1.3.0.zip(r-4.4)MGnifyR_1.1.0.zip(r-4.3)
MGnifyR_1.3.0.tgz(r-4.4-any)MGnifyR_1.1.0.tgz(r-4.3-any)
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MGnifyR.pdf |MGnifyR.html✨
MGnifyR/json (API)
NEWS

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

Peer review:

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

On BioConductor:MGnifyR-1.3.0(bioc 3.21)MGnifyR-1.2.0(bioc 3.20)

infrastructuredataimportmetagenomics

7.85 score 19 stars 31 scripts 180 downloads 32 exports 178 dependencies

Last updated 23 days agofrom:c8f32c3ae7. Checks:OK: 1 WARNING: 3 NOTE: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-winWARNINGNov 01 2024
R-4.5-linuxWARNINGNov 01 2024
R-4.4-winWARNINGNov 01 2024
R-4.4-macNOTENov 01 2024
R-4.3-winNOTESep 22 2024
R-4.3-macNOTESep 22 2024

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:abindapeaskpassassertthatassortheadbackportsbase64encbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocGenericsBiocNeighborsBiocParallelBiocSingularBiostringsblusterbootbslibcachemCairocheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIDECIPHERdecontamDelayedArrayDelayedMatrixStatsdigestDirichletMultinomialdplyrdqrngevaluatefansifarverfastmapFNNfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetshttrigraphIRangesirlbaisobandjquerylibjsonliteknitrlabelinglambda.rlatticelazyevallifecyclelme4lpSolvemagrittrMASSMatrixMatrixGenericsmatrixStatsmediationmemoisemgcvmiamimeminqaMultiAssayExperimentmunsellmvtnormnlmenloptrnnetopensslopenxlsxpermutepheatmappillarpkgconfigplyrpngpurrrR.methodsS3R.ooR.utilsR6raggrappdirsrbiomRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppParallelRcppProgressreshape2rjsonrlangrmarkdownrpartRSpectrarstudioapirsvdRtsneS4ArraysS4VectorssandwichsassScaledMatrixscalesscaterscuttleSingleCellExperimentsitmoslamsnowSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyjsontidyrtidyselecttidytreetinytextreeioTreeSummarizedExperimenttriebeardUCSC.utilsurltoolsutf8uwotvctrsveganviporviridisviridisLitewithrxfunXVectoryamlyulab.utilszipzlibbioczoo

MGnifyR

Rendered fromMGnifyR.Rmdusingknitr::rmarkdownon Nov 01 2024.

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

MGnifyR, extended vignette

Rendered fromMGnifyR_long.Rmdusingknitr::rmarkdownon Nov 01 2024.

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

Metagenomics bioinformatics at MGnify

Rendered fromMGnify_course.Rmdusingknitr::rmarkdownon Nov 01 2024.

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

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