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Classification tools for haematological diseases
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README.md

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.

Installation

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!

Using hemaClass

Please confer the vignette to hemaClass which can be found via vignette("howto") or on the help page at hemaclass.org. It can also be directly read at github.

References

  1. Steffen Falgreen, Anders Ellern Bilgrau, Jonas Have; "hemaClass: Online classification of gene expression profiles in hematological cancers." (2014) http://github.com/falgreen/hemaClass

  2. 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)

  3. 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)

  4. 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.

  5. 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.

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