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:Lucas schiffer [aut, cre], Levi Waldron [aut], Edoardo Pasolli [ctb], Jennifer Wokaty [ctb], Sean Davis [ctb], Audrey Renson [ctb], Chloe Mirzayi [ctb], Paolo Manghi [ctb], Samuel Gamboa-Tuz [ctb], Marcel Ramos [ctb], Valerie Obenchain [ctb], Kelly Eckenrode [ctb], Nicola Segata [ctb], Tuomas Borman [ctb], Sehyun Oh [ctb], Yoon-Ji Jung [ctb], NCI [fnd]

curatedMetagenomicData_3.21.1.tar.gz
curatedMetagenomicData_3.21.1.zip(r-4.7)curatedMetagenomicData_3.21.1.zip(r-4.6)curatedMetagenomicData_3.21.1.zip(r-4.5)
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✨
card.svg |card.png
curatedMetagenomicData/json (API)
NEWS

# 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:

On CRAN:

Conda:

experimenthubhomo_sapiens_datamicrobiomedatareproducibleresearchbioconductorbioconductor-packager01ca230551

7.37 score 154 stars 380 scripts 3 exports 144 dependencies

Last updated from:cecdfeca42. Checks:8 ERROR, 1 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR531
source / vignettesERROR380
linux-release-x86_64ERROR573
macos-release-arm64ERROR475
macos-oldrel-arm64ERROR480
windows-develERROR561
windows-releaseERROR538
windows-oldrelERROR489
wasm-releaseOK198

Exports:curatedMetagenomicDatamergeDatareturnSamples

Dependencies:abindAnnotationDbiAnnotationHubapeaskpassassortheadbase64encbeachmatbeeswarmBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocManagerBiocNeighborsBiocParallelBiocSingularBiocVersionBiostringsbitbit64blobblustercachemCairocliclustercodetoolscpp11crayoncurlDBIdbplyrDECIPHERdecontamDelayedArrayDelayedMatrixStatsdigestDirichletMultinomialdplyrdqrngecodiveExperimentHubfarverfastmapfilelockFNNformatRfsfutile.loggerfutile.optionsgenericsGenomicRangesggbeeswarmggplot2ggrastrggrepelgluegridExtragtablehttrhttr2igraphIRangesirlbaisobandjsonliteKEGGRESTlabelinglambda.rlatticelazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmiamimeMultiAssayExperimentnlmeopensslpermutepheatmappillarpkgconfigplyrpngpurrrR6raggrappdirsRColorBrewerRcppRcppAnnoyRcppEigenRcppMLRcppProgressreshape2rlangRSpectraRSQLitersvdRtsneS4ArraysS4VectorsS7ScaledMatrixscalesscaterscuttleSeqinfoSingleCellExperimentsitmosnowSparseArraysparseMatrixStatsstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselecttidytreetreeioTreeSummarizedExperimentutf8uwotvctrsveganviporviridisviridisLitewithrXVectoryamlyulab.utils