Package: OmicsMLRepoR 1.1.0
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:
OmicsMLRepoR_1.1.0.tar.gz
OmicsMLRepoR_1.1.0.zip(r-4.5)OmicsMLRepoR_1.1.0.zip(r-4.4)
OmicsMLRepoR_1.1.0.tgz(r-4.4-any)
OmicsMLRepoR_1.1.0.tar.gz(r-4.5-noble)OmicsMLRepoR_1.1.0.tar.gz(r-4.4-noble)
OmicsMLRepoR_1.1.0.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
- mini_cmd - A subset of cMD metadata
- sample_metadata - Sample_metadata
On BioConductor:OmicsMLRepoR-0.99.3(bioc 3.20)
softwareinfrastructuredatarepresentation
Last updated 2 days agofrom:1269f9345e. Checks:OK: 1 NOTE: 4. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 30 2024 |
R-4.5-win | NOTE | Oct 30 2024 |
R-4.5-linux | NOTE | Oct 30 2024 |
R-4.4-win | NOTE | Oct 30 2024 |
R-4.4-mac | NOTE | Oct 30 2024 |
Exports:availableTermsget_ontologiesgetLongMetaTbgetMetadatagetNarrowMetaTbgetOntoInfogetShortMetaTbgetWideMetaTbmerge_vectorsontoTreePlottree_filter
Dependencies:askpassbase64encBiobaseBiocFileCacheBiocGenericsbitbit64blobbslibcachemclicliprcolorspacecpp11crayoncurldata.treeDBIdbplyrDiagrammeRdigestdplyrevaluatefansifarverfastmapfilelockfontawesomefsgenericsgluehighrhmshtmltoolshtmlwidgetshttrhttr2igraphjquerylibjsonliteknitrlabelinglatticelifecyclelubridatemagrittrMatrixmemoisemimemunsellopensslpillarpkgconfigplogrplyrprettyunitsprogresspurrrR6rappdirsRColorBrewerRcppreadrrlangrmarkdownrolsRSQLiterstudioapisassscalesstringistringrsystibbletidyrtidyselecttimechangetinytextzdbutf8vctrsviridisLitevisNetworkvroomwithrxfunyaml
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 cMD metadata | mini_cmd |
OmicsMLRepoR: A package for browsing harmonized metadata through ontology | OmicsMLRepoR |
Plot ontology tree | ontoTreePlot |
sample_metadata | sample_metadata |
Keep rows that include the queried terms and their descendants | tree_filter |