Other packages > Find by keyword >

Allspice  

RNA-Seq Profile Classifier
View on CRAN: Click here


Download and install Allspice package within the R console
Install from CRAN:
install.packages("Allspice")

Install from Github:
library("remotes")
install_github("cran/Allspice")

Install by package version:
library("remotes")
install_version("Allspice", "1.0.7")



Attach the package and use:
library("Allspice")
Maintained by
Ville-Petteri Makinen
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-02-18
Latest Update: 2023-01-20
Description:
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, . 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.
How to cite:
Ville-Petteri Makinen (2022). Allspice: RNA-Seq Profile Classifier. R package version 1.0.7, https://cran.r-project.org/web/packages/Allspice. Accessed 15 Jul. 2026.
Previous versions and publish date:
1.0.2 (2022-02-18 21:30), 1.0.3 (2022-02-22 10:10), 1.0.4 (2022-04-13 07:12), 1.0.5 (2022-06-11 12:40), 1.0.6 (2022-12-15 07:10), (2026-07-09 07:57)
Other packages that cited Allspice R package
View Allspice citation profile
Other R packages that Allspice depends, imports, suggests or enhances
Complete documentation for Allspice
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

gscaLCA  
Generalized Structure Component Analysis- Latent Class Analysis & Latent Class Regression
Execute Latent Class Analysis (LCA) and Latent Class Regression (LCR) by using Generalized Structu ...
Download / Learn more Package Citations See dependency  
pulseTD  
Identification of Transcriptional Dynamics using Pulse Models via 4su-Seq Data and RNA-Seq Data
A tool for analyzing the transcription, processing and degradation rates of genes by 4sU-seq (the Me ...
Download / Learn more Package Citations See dependency  
SECFISH  
Disaggregate Variable Costs
These functions were developed within SECFISH project (Strengthening regional cooperation in the are ...
Download / Learn more Package Citations See dependency  
footBayes  
Fitting Bayesian and MLE Football Models
This is the first package allowing for the estimation, visualization and prediction of the most wel ...
Download / Learn more Package Citations See dependency  
binhf  
Haar-Fisz Functions for Binomial Data
Binomial Haar-Fisz transforms for Gaussianization as in Nunes and Nason (2009). ...
Download / Learn more Package Citations See dependency  
PermAlgo  
Permutational Algorithm to Simulate Survival Data
This version of the permutational algorithm generates a dataset in which event and censoring times ...
Download / Learn more Package Citations See dependency  

27,806

R Packages

239,283

Dependencies

73,837

Author Associations

27,807

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA