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devtools::load_all(".")
##  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"