Package: OmicsMLRepoR 1.1.5

Sehyun Oh

OmicsMLRepoR: Search harmonized metadata created under the OmicsMLRepo project

This package provides functions to browse the harmonized metadata for large omics databases. This package also supports data navigation if the metadata incorporates ontology.

Authors:Sehyun Oh [aut, cre], Kaelyn Long [aut]

OmicsMLRepoR_1.1.5.tar.gz
OmicsMLRepoR_1.1.5.zip(r-4.5)OmicsMLRepoR_1.1.5.zip(r-4.4)
OmicsMLRepoR_1.1.5.tgz(r-4.5-any)OmicsMLRepoR_1.1.5.tgz(r-4.4-any)
OmicsMLRepoR_1.1.5.tar.gz(r-4.5-noble)OmicsMLRepoR_1.1.5.tar.gz(r-4.4-noble)
OmicsMLRepoR_1.1.5.tgz(r-4.4-emscripten)
OmicsMLRepoR.pdf |OmicsMLRepoR.html✨
OmicsMLRepoR/json (API)
NEWS

# Install 'OmicsMLRepoR' in R:

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

Bug tracker:https://github.com/shbrief/omicsmlrepor/issues

Datasets:

mini_cbio - A subset of cBioPortalData metadata
mini_cmd - A subset of cMD metadata
mini_cmd2 - A subset of cMD metadata
mini_cmd3 - A subset of cMD metadata
sample_metadata - Sample_metadata

On BioConductor:OmicsMLRepoR-1.1.2(bioc 3.21)OmicsMLRepoR-1.0.0(bioc 3.20)

software infrastructure datarepresentation u24ca289073

5.40 score 14 scripts 120 downloads 13 exports 87 dependencies

Last updated 16 hours agofrom:cd56020c02. Checks:1 OK, 6 NOTE. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 23 2025
R-4.5-win	NOTE	Mar 23 2025
R-4.5-mac	NOTE	Mar 23 2025
R-4.5-linux	NOTE	Mar 23 2025
R-4.4-win	NOTE	Mar 23 2025
R-4.4-mac	NOTE	Mar 23 2025
R-4.4-linux	NOTE	Mar 23 2025

Exports:availableTerms get_ontologies getLongMetaTb getMetadata getNarrowMetaTb getOntoInfo getShortMetaTb getWideMetaTb merge_vectors ontoSummarize ontoTreePlot spreadMeta tree_filter

Dependencies:askpass base64enc Biobase BiocFileCache BiocGenerics bit bit64 blob bslib cachem cli clipr colorspace cpp11 crayon curl data.tree DBI dbplyr DiagrammeR digest dplyr evaluate fansi farver fastmap filelock fontawesome fs generics glue highr hms htmltools htmlwidgets httr httr2 igraph jquerylib jsonlite knitr labeling lattice lifecycle lubridate magrittr Matrix memoise mime munsell openssl pillar pkgconfig plogr plyr prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp readr rlang rmarkdown rols RSQLite rstudioapi sass scales stringi stringr sys tibble tidyr tidyselect timechange tinytex tzdb utf8 vctrs viridisLite visNetwork vroom withr xfun yaml

OmicsMLRepoR - Quickstart

Sehyun Oh, Kaelyn Long

Rendered fromQuickstart.Rmdusingknitr::rmarkdownon Mar 23 2025.

Last update: 2025-03-22
Started: 2024-07-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Extract all the terms used in a quired attribute/column	availableTerms
Extract ontology from the ontology term ids	get_ontologies
Expands metadata with multiple values belong to a same attribute	getLongMetaTb
Download a harmonized metadata table	getMetadata
Collapse values from multiple columns into one	getNarrowMetaTb
Query Ontology Lookup Service (OLS)	getOntoInfo
Compresses expanded metadata columns to one row per sample	getShortMetaTb
Create individual columns for different attributes stored in one column	getWideMetaTb
Custom function to merge vectors	merge_vectors
A subset of cBioPortalData metadata	mini_cbio
A subset of cMD metadata	mini_cmd
A subset of cMD metadata	mini_cmd2
A subset of cMD metadata	mini_cmd3
OmicsMLRepoR: A package for browsing harmonized metadata through ontology	OmicsMLRepoR
Groups ontology terms by the child term of a provided "parent" they fall under	ontoSummarize
Plot ontology tree	ontoTreePlot
sample_metadata	sample_metadata
Manipulate metadata into a spread format	spreadMeta
Keep rows that include the queried terms and their descendants	tree_filter