Package: HMP16SData 1.32.0

Lucas schiffer

HMP16SData: 16S rRNA Sequencing Data from the Human Microbiome Project

HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub.

Authors:Lucas schiffer [aut, cre], Rimsha Azhar [aut], Marcel Ramos [ctb], Ludwig Geistlinger [ctb], Levi Waldron [aut]

HMP16SData_1.32.0.tar.gz
HMP16SData_1.32.0.tar.gz(r-4.7-any)HMP16SData_1.32.0.tar.gz(r-4.6-any)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
HMP16SData/json (API)

# Install 'HMP16SData' in R:

install.packages('HMP16SData', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/waldronlab/hmp16sdata/issues

Datasets:

dictionary - A data dictionary describing dbGaP metadata variables

On BioConductor:HMP16SData-1.33.1(data/experiment 3.24)HMP16SData-1.32.0(data/experiment 3.23)

experimentdata experimenthub homo_sapiens_data microbiomedata reproducibleresearch sequencingdata bioconductor bioconductor-package hmp r01ca230551 datapkg

6.55 score 11 stars 46 scripts 7 exports 100 dependencies

Last updated from:815437aefc (on RELEASE_3_23). Checks:1 WARNING, 3 OK. Indexed: no.

This is a data package. Data packages may be large and do not get checked across all platforms.

Target	Result	Time
bioc-checks	WARNING	190
linux-devel	OK	434
source / vignettes	OK	406
linux-release	OK	447

Exports:%>%as_phyloseq attach_dbGaP kable_one table_one V13 V35

Dependencies:abind AnnotationDbi AnnotationHub askpass assertthat base64enc Biobase BiocBaseUtils BiocFileCache BiocGenerics BiocManager BiocVersion Biostrings bit bit64 blob bslib cachem cli clipr cpp11 crayon curl DBI dbplyr DelayedArray digest dplyr evaluate ExperimentHub farver fastmap filelock fontawesome fs generics GenomicRanges glue highr hms htmltools httr httr2 IRanges jquerylib jsonlite kableExtra KEGGREST knitr labeling lattice lifecycle magrittr Matrix MatrixGenerics matrixStats memoise mime openssl pillar pkgconfig png prettyunits progress purrr R6 rappdirs RColorBrewer readr rlang rmarkdown RSQLite rstudioapi S4Arrays S4Vectors sass scales Seqinfo SparseArray stringi stringr SummarizedExperiment svglite sys systemfonts textshaping tibble tidyr tidyselect tinytex tzdb utf8 vctrs viridisLite vroom withr xfun xml2 XVector yaml

HMP16SData

Rendered fromHMP16SData.Rmdusingknitr::rmarkdown

Last update: 2021-05-18
Started: 2017-10-06

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Coerce a SummarizedExperiment object to a phyloseq object	as_phyloseq
Attach dbGaP metadata to a SummarizedExperiment object	attach_dbGaP
A data dictionary describing dbGaP metadata variables	dictionary
16S rRNA sequencing data from the Human Microbiome Project	HMP16SData
Produce a summary HTML table of key demographic variables	kable_one
Produce a summary data.frame of key demographic variables	table_one
HMP 16S rRNA sequencing data for variable regions 1–3	V13
HMP 16S rRNA sequencing data for variable regions 3–5	V35