What curatedMetagenomicData provides | Additional documentation and resources | Installation | R Packages | Sample Metadata | Data Access | curatedMetagenomicData() | mergeData() | returnSamples() | Example Analysis | Load R packages | Retrieve harmonized metadata | Prepare Data | Return Samples | Agglomerate By Taxonomic Rank | Alpha Diversity | Beta Diversity | Bray–Curtis PCoA | UMAP | Differential Abundance | Type Conversion | Session Info
Package: curatedMetagenomicData 3.21.1
Lucas schiffer
curatedMetagenomicData: Curated Metagenomic Data of the Human Microbiome
The curatedMetagenomicData package provides standardized, curated human microbiome data for novel analyses. It includes gene families, marker abundance, marker presence, pathway abundance, pathway coverage, and relative abundance for samples collected from different body sites. The bacterial, fungal, and archaeal taxonomic abundances for each sample were calculated with MetaPhlAn3, and metabolic functional potential was calculated with HUMAnN3. The manually curated sample metadata and standardized metagenomic data are available as (Tree)SummarizedExperiment objects.
Authors:
curatedMetagenomicData_3.21.1.tar.gz
curatedMetagenomicData_3.21.1.zip(r-4.7-any)curatedMetagenomicData_3.21.1.zip(r-4.6-any)curatedMetagenomicData_3.21.1.zip(r-4.5-any)
curatedMetagenomicData_3.21.1.tgz(r-4.6-any)curatedMetagenomicData_3.21.1.tgz(r-4.5-any)
curatedMetagenomicData_3.21.1.tar.gz(r-4.7-any)curatedMetagenomicData_3.21.1.tar.gz(r-4.6-any)
curatedMetagenomicData_3.21.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
curatedMetagenomicData/json (API)
| # Install 'curatedMetagenomicData' in R: |
| install.packages('curatedMetagenomicData', repos = c('https://waldronlab.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/waldronlab/curatedmetagenomicdata/issues
Datasets:
- sampleMetadata - Manually Curated Sample Metadata
On BioConductor:curatedMetagenomicData-3.19.0(data/experiment 3.24)curatedMetagenomicData-3.20.0(data/experiment 3.23)
experimenthubhomo_sapiens_datamicrobiomedatareproducibleresearchbioconductorbioconductor-packager01ca230551
Last updated from:afd13adf72. Checks:7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | NOTE | 525 | ||
| source / vignettes | OK | 349 | ||
| linux-release | NOTE | 519 | ||
| macos-release | NOTE | 598 | ||
| macos-oldrel | NOTE | 427 | ||
| windows-devel | NOTE | 482 | ||
| windows-release | NOTE | 517 | ||
| windows-oldrel | NOTE | 490 | ||
| wasm-release | OK | 174 |
Exports:curatedMetagenomicDatamergeDatareturnSamples
Dependencies:abindAnnotationDbiAnnotationHubapeaskpassassortheadbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocNeighborsBiocParallelBiocSingularBiocVersionBiostringsbitbit64blobblustercachemcliclustercodetoolscpp11crayoncurlDBIdbplyrDECIPHERdecontamDelayedArrayDelayedMatrixStatsdigestDirichletMultinomialdplyrdqrngecodiveExperimentHubfarverfastmapfilelockFNNformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggbeeswarmggplot2ggrepelgluegridExtragtablehttrhttr2igraphIRangesirlbaisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmiamimeMultiAssayExperimentnlmeopensslpermutepheatmappillarpkgconfigplyrpngpurrrR6rappdirsrbibutilsRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressRdpackreshape2rlangRSpectraRSQLitersvdRtsneS4ArraysS4VectorsS7ScaledMatrixscalesscaterscuttleSeqinfoSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsystibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimentutf8uwotvctrsveganviporviridisviridisLitewithrXVectoryamlyulab.utils
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Access Curated Metagenomic Data | curatedMetagenomicData |
| Merge curatedMetagenomicData List | mergeData |
| Return Samples Across Studies | returnSamples |
| Manually Curated Sample Metadata | sampleMetadata |