Package: Allspice 1.0.7
Ville-Petteri Makinen
Allspice: RNA-Seq Profile Classifier
We developed a lightweight machine learning tool for RNA profiling of acute lymphoblastic leukemia (ALL), however, it can be used for any problem where multiple classes need to be identified from multi-dimensional data. The methodology is described in Makinen V-P, Rehn J, Breen J, Yeung D, White DL (2022) Multi-cohort transcriptomic subtyping of B-cell acute lymphoblastic leukemia, International Journal of Molecular Sciences 23:4574, <doi:10.3390/ijms23094574>. The classifier contains optimized mean profiles of the classes (centroids) as observed in the training data, and new samples are matched to these centroids using the shortest Euclidean distance. Centroids derived from a dataset of 1,598 ALL patients are included, but users can train the models with their own data as well. The output includes both numerical and visual presentations of the classification results. Samples with mixed features from multiple classes or atypical values are also identified.
Authors:
Allspice_1.0.7.tar.gz
Allspice_1.0.7.tar.gz(r-4.5-noble)Allspice_1.0.7.tar.gz(r-4.4-noble)
Allspice_1.0.7.tgz(r-4.4-emscripten)Allspice_1.0.7.tgz(r-4.3-emscripten)
Allspice.pdf |Allspice.html✨
Allspice/json (API)
| # Install 'Allspice' in R: |
| install.packages('Allspice', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org')) |
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 years agofrom:0c2e0b380d. Checks:OK: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 18 2024 |
| R-4.5-linux | OK | Dec 18 2024 |
Exports:assemble<-assetbcellALLclassifierclassifyconfigurationconfiguration<-covariates<-exportinformationnomenclature<-normalizepredictionsprofiles<-reportscoresstandardizevisuals<-
Dependencies:
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Finish Asset contents | assemble assemble,Asset-method assemble<- assemble<-,Asset-method |
| Constructor for Asset | asset Asset-class |
| Simulated data | bcellALL |
| Constructor for Classifier | classifier Classifier-class |
| Data classification | classify classify,Asset-method |
| Asset configuration | configuration configuration,Asset-method configuration<- configuration<-,Asset-method |
| Sample covariate data | covariates covariates,Classifier-method covariates<- covariates<-,Classifier-method |
| Data classification | export export,Asset-method |
| Classifier contents | information information,Classifier-method |
| Variable names | nomenclature nomenclature,Asset-method nomenclature<- nomenclature<-,Asset-method |
| Sample normalization | normalize normalize,Asset-method |
| Category predictions | predictions predictions,Classifier-method |
| Sample data profiles | profiles profiles<- profiles<-,Classifier-method |
| Visualization of results | report report,Classifier-method |
| Category scores | scores scores,Classifier-method |
| Data standardization | standardize standardize,Asset-method |
| Visual attributes | visuals visuals,Asset-method visuals<- visuals<-,Asset-method |