Package: MGnifyR 1.1.0

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_1.1.0.tar.gz
MGnifyR_1.1.0.zip(r-4.5)MGnifyR_1.1.0.zip(r-4.4)MGnifyR_1.1.0.zip(r-4.3)
MGnifyR_1.1.0.tgz(r-4.4-any)MGnifyR_1.1.0.tgz(r-4.3-any)
MGnifyR_1.1.0.tar.gz(r-4.5-noble)MGnifyR_1.1.0.tar.gz(r-4.4-noble)
MGnifyR_1.1.0.tgz(r-4.4-emscripten)MGnifyR_1.1.0.tgz(r-4.3-emscripten)
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'))

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

On BioConductor:MGnifyR-1.1.0(bioc 3.20)MGnifyR-1.0.0(bioc 3.19)

bioconductor-package

32 exports 1.75 score 178 dependencies

Last updated 2 months agofrom:e8c773f606

Exports:authTok authTok<-cacheDir cacheDir<-clearCache clearCache<-databaseUrl databaseUrl<-doQuery getData getFile getMetadata getResult 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 MgnifyClient searchAnalysis searchFile showWarnings showWarnings<-useCache useCache<-verbose verbose<-

Dependencies:abind ape askpass assertthat backports base64enc beachmat beeswarm BH Biobase BiocBaseUtils BiocGenerics BiocNeighbors BiocParallel BiocSingular Biostrings bluster boot bslib cachem Cairo checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI DECIPHER decontam DelayedArray DelayedMatrixStats digest DirichletMultinomial dplyr dqrng evaluate fansi farver fastmap FNN fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggbeeswarm ggplot2 ggrastr ggrepel glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr igraph IRanges irlba isoband jquerylib jsonlite knitr labeling lambda.r lattice lazyeval lifecycle lme4 lpSolve magrittr MASS Matrix MatrixGenerics matrixStats mediation memoise mgcv mia mime minqa MultiAssayExperiment munsell mvtnorm nlme nloptr nnet openssl openxlsx permute pheatmap pillar pkgconfig plyr png purrr R.methodsS3 R.oo R.utils R6 ragg rappdirs rbiom RColorBrewer Rcpp RcppAnnoy RcppEigen RcppHNSW RcppML RcppParallel RcppProgress reshape2 rjson rlang rmarkdown rpart RSpectra rstudioapi rsvd Rtsne S4Arrays S4Vectors sandwich sass ScaledMatrix scales scater scuttle SingleCellExperiment sitmo slam snow SparseArray sparseMatrixStats stringi stringr SummarizedExperiment sys systemfonts textshaping tibble tidyjson tidyr tidyselect tidytree tinytex treeio TreeSummarizedExperiment triebeard UCSC.utils urltools utf8 uwot vctrs vegan vipor viridis viridisLite withr xfun XVector yaml yulab.utils zip zlibbioc zoo

MGnifyR

Rendered fromMGnifyR.Rmdusingknitr::rmarkdownon Jun 24 2024.

Last update: 2024-03-28
Started: 2020-09-11

MGnifyR, extended vignette

Rendered fromMGnifyR_long.Rmdusingknitr::rmarkdownon Jun 24 2024.

Last update: 2024-03-28
Started: 2023-10-30

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Development and contributors

Readme and manuals

Help Manual

Help page	Topics
'MGnifyR' Package.	MGnifyR-package MGnifyR
MgnifyClient accessors and mutators	authTok 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 results	getData getData,MgnifyClient-method
Download any MGnify files, also including processed reads and identified protein sequences	getFile getFile,MgnifyClient-method searchFile searchFile,MgnifyClient-method
Get all Study, Sample and Analysis metadata for the supplied analyses accessions	getMetadata getMetadata,MgnifyClient-method
Get microbial and/or functional profiling data for a list of accessions	getResult 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 accessions	searchAnalysis searchAnalysis,MgnifyClient-method