Sample Type & Platform Info
Vanessa Mengze Li
05/15/2025
SampleType.Rmd
devtools::load_all(".")
## ℹ Loading OmicSignature
We use BRENDA tissue ontology to indicate the tissue or cell-line of
a signature. BRENDA tissue ontology version: 10/2021.
The OBO file was downloaded at https://www.brenda-enzymes.org/ontology.php.
To ensure accurate documentation of the technologies used in the
experiment, we provided a predefined list of experimental
platforms.
If you are not sure which BRENDA tissue ontology or platform name to use, you can search for them.
Search for sample type and platform
Multiple search terms are seperated by space ” “. The search is case
in-sensitive.
Set contain_all = TRUE
to show results include all search
terms.
Set contain_all = FALSE
to show results include any of the
search terms.
searchSampleType("mcf cell", contain_all = TRUE)
## ID Name
## 95 BTO:0000093 MCF-7 cell
## 1939 BTO:0001939 MCF-10A cell
## 2270 BTO:0002270 MCF-7/2a cell
## 2544 BTO:0002544 MCF-12A cell
## 2545 BTO:0002545 MCF-12F cell
## 3900 BTO:0003900 MCF-10F cell
## 5124 BTO:0005127 MCF-10A neoT cell
## 5189 BTO:0005192 MCF-7/adr cell
## 5967 BTO:0005970 MCF-7/LCC9 cell
## 6395 BTO:0006398 MCF-10-2A cell
searchSampleType("MCF-10 MCF-7", contain_all = FALSE)
## ID Name
## 95 BTO:0000093 MCF-7 cell
## 2270 BTO:0002270 MCF-7/2a cell
## 5189 BTO:0005192 MCF-7/adr cell
## 5967 BTO:0005970 MCF-7/LCC9 cell
## 1939 BTO:0001939 MCF-10A cell
## 3900 BTO:0003900 MCF-10F cell
## 5124 BTO:0005127 MCF-10A neoT cell
## 6395 BTO:0006398 MCF-10-2A cell
Search for a single word:
searchPlatform("proteomics")
## [1] "proteomics by array"
## [2] "proteomics by mass spectrometry"
## [3] "proteomics by NMR"
## [4] "proteomics by antibody or aptamer"
## [5] "proteomics by fluorescence"
## [6] "single-cell proteomics by mass spectrometry"
Search for multiple words:
searchPlatform(c("transcript", "single-cell"), contain_all = TRUE)
## [1] "transcriptomics by single-cell RNA-seq"
## [2] "single-cell spatial transcriptomics"
If contain_all = FALSE
, results matching any of the key
words will be returned.
searchPlatform(c("transcript", "single-cell"), contain_all = FALSE)
## [1] "transcriptomics by single-cell RNA-seq"
## [2] "single-cell spatial transcriptomics"
## [3] "single-cell proteomics by mass spectrometry"
## [4] "single-cell CITE-seq"
## [5] "transcriptomics by array"
## [6] "transcriptomics by bulk RNA-seq"
## [7] "transcriptomics by long-read sequencing"
## [8] "ribosome transcriptomics"
## [9] "spatial transcriptomics"