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_1.3.0.tgz(r-4.4-any)
MGnifyR_1.3.0.tar.gz(r-4.5-noble)MGnifyR_1.3.0.tar.gz(r-4.4-noble)
MGnifyR_1.3.0.tgz(r-4.4-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-1.3.0(bioc 3.21)MGnifyR-1.2.0(bioc 3.20)

infrastructure dataimport metagenomics

7.68 score 20 stars 32 scripts 209 downloads 32 exports 160 dependencies

Last updated 4 months agofrom:c8f32c3ae7. Checks:1 OK, 4 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Jan 30 2025
R-4.5-win	NOTE	Jan 30 2025
R-4.5-linux	NOTE	Jan 30 2025
R-4.4-win	NOTE	Jan 30 2025
R-4.4-mac	NOTE	Jan 30 2025

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 assorthead beachmat beeswarm BH Biobase BiocBaseUtils BiocGenerics BiocNeighbors BiocParallel BiocSingular Biostrings bit bit64 bluster Cairo cellranger cli clipr cluster codetools colorspace commonmark cpp11 crayon curl DBI DECIPHER decontam DelayedArray DelayedMatrixStats digest DirichletMultinomial dplyr dqrng emmeans estimability fansi farver fillpattern FNN formatR fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggbeeswarm ggnewscale ggplot2 ggrastr ggrepel ggtext glue gridExtra gridtext gtable hms httr igraph IRanges irlba isoband jpeg jsonlite labeling lambda.r lattice lazyeval lifecycle magrittr markdown MASS Matrix MatrixGenerics matrixStats mgcv mia mime MultiAssayExperiment munsell mvtnorm nlme numDeriv openssl parallelly patchwork permute pheatmap pillar pkgconfig plyr png prettyunits progress purrr R6 ragg rbiom RColorBrewer Rcpp RcppAnnoy RcppEigen RcppML RcppProgress readr readxl rematch reshape2 rlang RSpectra rsvd Rtsne S4Arrays S4Vectors ScaledMatrix scales scater scuttle SingleCellExperiment sitmo slam snow SparseArray sparseMatrixStats stringi stringr SummarizedExperiment sys systemfonts textshaping tibble tidyjson tidyr tidyselect tidytree treeio TreeSummarizedExperiment triebeard tzdb UCSC.utils urltools utf8 uwot vctrs vegan vipor viridis viridisLite vroom withr xfun xml2 XVector yulab.utils

MGnifyR

Rendered fromMGnifyR.Rmdusingknitr::rmarkdownon Jan 30 2025.

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

MGnifyR, extended vignette

Rendered fromMGnifyR_long.Rmdusingknitr::rmarkdownon Jan 30 2025.

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

Metagenomics bioinformatics at MGnify

Rendered fromMGnify_course.Rmdusingknitr::rmarkdownon Jan 30 2025.

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

Citation

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 analysis 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