hemaClass: Classification tool for haematological diseases
The package hemaClass for the programming language R is a set of tools used for classification of hematological cancers using DNA microarrays. The package features one-by-one and reference based RMA normalisation, a proposed alternatives to regular cohort based RMA normalization, and oncogenomic classification and prediction of drug resistance of Diffuse Large B-Cell Lymphomas (DLBCL) and Multiple Myeloma (MM).
An easy-to-use shiny web application is incorporated into the package and available online at hemaclass.org or as a local instance via
runHemaClass() in R. The hemaClass package can naturally also be used programatically as a regular R-package.
Please do not hessitate to report bugs, suggestions, comments, and other issues for the hemaClass website or package via
bug.report(package = "hemaClass").
The currently only featured platform is Affymetrix GeneChip HG-U133 Plus 2.0 (
"u133plus2") but more are planned.
If you wish to install the latest version of
hemaClass directly from the master branch here at GitHub, run
# Install necessary packages # First from bioconductor source("http://bioconductor.org/biocLite.R") biocLite(c("affy", "affyio", "preprocessCore")) # Then from CRAN install.packages(c("shiny", "matrixStats", "Rcpp", "RcppArmadillo", "testthat", "WriteXLS", "RLumShiny", "gdata", "devtools")) # From GitHub and finally the package: devtools::install_github("AnalytixWare/ShinySky") devtools::install_github("oncoclass/hemaClass", dependencies = TRUE, build_vignettes = TRUE)
hemaClass is still under development and should be considered unstable. Be sure that you have the package development prerequisites if you wish to install the package from the source.
Note: The interface and function names may still see significant changes and modifications!
Steffen Falgreen, Anders Ellern Bilgrau, Jonas Have; "hemaClass: Online classification of gene expression profiles in hematological cancers." (2014) http://github.com/falgreen/hemaClass
Steffen Falgreen, Anders Ellern Bilgrau, Rasmus Froberg Brøndum, Lasse Hjort Jakobsen, Jonas Have, Kasper Lindblad Nielsen, Tarec Christoffer El-Galaly, Julie Støve Bøker, Alexander Schmitz, Hans Erik Johnsen, Karen Dybkær, and Martin Bøgsted; hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine. PLoS ONE Vol. 11, Issue 10 (2016)
Dybkær K, Bøgsted M, Falgreen S, Bødker JS et al. "Diffuse Large B-cell Lymphoma Classification System That Associates Normal B-cell Subset Phenotypes with Prognosis." Journal of Clinical Oncology 33, no. 12 (2015): 1379-1388. (GSE56315)
Falgreen S, Dybkær K, Young KH, Xu-Monette ZY et al. "Predicting response to multidrug regimens in cancer patients using cell line experiments and regularised regression models." BMC cancer 15, no. 1 (2015): 235.
Laursen, MB, Falgreen S, Bødker JS, Schmitz A, et al. "Human B-cell cancer cell lines as a preclinical model for studies of drug effect in diffuse large B-cell lymphoma and multiple myeloma." Experimental Hematology 42, no. 11 (2014): 927-938.