Sample Type & Platform Info

devtools::load_all(".")

## ℹ Loading OmicSignature

We use BRENDA tissue ontology to indicate the tissue or cell-line of a signature, and GEO platform accession id for platform records.
BRENDA tissue ontology version: 10/2021. The OBO file was downloaded at https://www.brenda-enzymes.org/ontology.php.
GEO platform IDs are manually downloaded at https://www.ncbi.nlm.nih.gov/geo/browse/?view=platforms. 25,827 platforms were downloaded as of 2024/02.
If you are not sure which BRENDA tissue ontology or GEO platform accession id to use, you can search for them as shown below.

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
## 94   BTO:0000093        MCF-7 cell
## 1938 BTO:0001939      MCF-10A cell
## 2269 BTO:0002270     MCF-7/2a cell
## 2543 BTO:0002544      MCF-12A cell
## 2544 BTO:0002545      MCF-12F cell
## 3899 BTO:0003900      MCF-10F cell
## 5123 BTO:0005127 MCF-10A neoT cell
## 5188 BTO:0005192    MCF-7/adr cell
## 5966 BTO:0005970   MCF-7/LCC9 cell
## 6394 BTO:0006398    MCF-10-2A cell

searchSampleType("MCF-10 MCF-7", contain_all = FALSE)

##               ID              Name
## 94   BTO:0000093        MCF-7 cell
## 2269 BTO:0002270     MCF-7/2a cell
## 5188 BTO:0005192    MCF-7/adr cell
## 5966 BTO:0005970   MCF-7/LCC9 cell
## 1938 BTO:0001939      MCF-10A cell
## 3899 BTO:0003900      MCF-10F cell
## 5123 BTO:0005127 MCF-10A neoT cell
## 6394 BTO:0006398    MCF-10-2A cell

searchPlatform("illumina hiseq 3000", organism = "Homo Sapiens", contain_all = TRUE)

##       Accession
## 2681   GPL31935
## 3776   GPL30008
## 5877   GPL27044
## 6015   GPL26864
## 7794   GPL24496
## 8304   GPL23888
## 10569  GPL21290
##                                                                           Name
## 2681                          Illumina HiSeq 3000 (Homo sapiens; Myxoma virus)
## 3776    Illumina HiSeq 3000 (Homo sapiens; Human T-cell leukemia virus type I)
## 5877                                        Illumina Hiseq 3000 (Homo sapiens)
## 6015  Illumina HiSeq 3000 (Canis lupus familiaris; Homo sapiens; Mus musculus)
## 7794                          Illumina HiSeq 3000 (Homo sapiens; Mus musculus)
## 8304              Illumina HiSeq 3000 (Homo sapiens; Human gammaherpesvirus 8)
## 10569                                       Illumina HiSeq 3000 (Homo sapiens)
##                       Technology
## 2681  high-throughput sequencing
## 3776  high-throughput sequencing
## 5877  high-throughput sequencing
## 6015  high-throughput sequencing
## 7794  high-throughput sequencing
## 8304  high-throughput sequencing
## 10569 high-throughput sequencing
##                                               Organism
## 2681                         Homo sapiens;Myxoma virus
## 3776   Homo sapiens;Human T-cell leukemia virus type I
## 5877                                      Homo sapiens
## 6015  Canis lupus familiaris;Homo sapiens;Mus musculus
## 7794                         Homo sapiens;Mus musculus
## 8304             Homo sapiens;Human gammaherpesvirus 8
## 10569                                     Homo sapiens

Show only accession id:

searchPlatform("illumina hiseq 3000", organism = "Homo Sapiens", contain_all = TRUE, accession_only = TRUE)

## [1] "GPL31935" "GPL30008" "GPL27044" "GPL26864" "GPL24496" "GPL23888" "GPL21290"

Vanessa Mengze Li

10/17/2024

Search for sample type and platform