README.md

In HaemAalborg/hemaClass: One-by-one normalization and classification of hematological malignacies

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.aau.dk 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 standard BAGS and REGS implemented in the shiny GUI only supports Affymetrix GeneChip HG-U133 Plus 2.0 ("u133plus2"). Prediction of BAGS classes uses nanostring data is supported in the R terminal with the BAGS2clinic() function.

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
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(c("affy", "affyio", "preprocessCore"))

# Then from CRAN
install.packages(c("shiny", "matrixStats", "Rcpp", "RcppArmadillo", "stringi",
                   "testthat", "WriteXLS", "RLumShiny", "gdata", "devtools"))

# From GitHub and finally the package:
devtools::install_github("AnalytixWare/ShinySky")
devtools::install_github("HaemAalborg/hemaClass", build = TRUE, build_opts = c("--no-resave-data", "--no-manual"))

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.aau.dk. 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 Broendum, Lasse Hjort Jakobsen, Jonas Have, Kasper Lindblad Nielsen, Tarec Christoffer El-Galaly, Julie Stoeve Boedker, Alexander Schmitz, Hans Erik Johnsen, Karen Dybkaer, and Martin Boegsted; "hemaClass.org: Online One-By-One Microarray Normalization and Classification of Hematological Cancers for Precision Medicine."" PLoS ONE Vol. 11, Issue 10 (2016)

3. Dybkaer K, Boegsted M, Falgreen S, Boedker 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, Dybkaer 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, Boedker 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.

6. Michaelsen, T. Y. et al. (2018) "A B-cell-associated gene signature classification of diffuse large B-cell lymphoma by NanoString technology." Blood advances, 2(13): 1542-1546.

HaemAalborg/hemaClass documentation built on Oct. 22, 2019, 7:01 p.m.