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DESCRIPTION 100644 1 kb
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README.txt 100755 3 kb
GISPA: A Method for Gene Integrated Set Profile Analysis ======================================================== Authors _______ Bhakti Dwivedi & Jeanne Kowalski Maintainer __________ Bhakti Dwivedi Organization ____________ Biostatistics & Bioinformatics Shared Resource Winship Cancer Institute Emory University Atlanta, GA 30322 Purpose _______ Gene Integrated Set Profile Analysis (GISPA) is a method intended for the researchers who are interested in defining gene sets with similar, a priori specified molecular profile. GISPA method has been previosuly published in Nucleic Acids Research journal (Kowalski et al., 2016; PMID: 26826710). Prerequisites -------------- 1) Download and install R or RStudio (version 3.1.2. or later) from https://cran.r-project.organd 2) Open R and install the required R packages: install.packages( c("ggplot2", "genefilter", "changepoint", "HH", "latticeExtra", "scatterplot3d", "data.table", "plyr", "knitr") ) Installation ------------ if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("GISPA") Running GISPA from the GitHub ----------------------------- Users can run GISPA locally by downloading the source code available from the GitHub: Vignette ------------ You can find the vignette for `GISPA` under [/vignettes/GISPA_manual.Rmd] Bug Reports/Questions _____________________ Please contact Bhakti Dwivedi, for questions, comments, or feature requests. Funding _______ This work is funded by the Leukemia and Lymphoma Society Translational Research Program Award (to Jeanne Kowalski); Georgia Research Alliance Scientist Award (Jeanne Kowalski); a Team Science Seed Funding from the Winship Cancer Institute of Emory University (Lawrence H. Boise, Sagar Lonial, Michael R. Rossi); Biostatistics and Bioinformatics Shared Resource of Winship Cancer Institute of Emory University and NIH/NCI [Award number P30CA138292, in part]. The content is solely the responsibility of the authors and does not necessarily represent the official views of the NIH. Citation ________ Kowalski J, Dwivedi B, Newman S, Switchenko JM, Pauly R, Gutman DA, Arora J, Gandhi K, Ainslie K, Doho G, Qin Z, Moreno CS, Rossi MR, Vertino PM, Lonial S, Bernal-Mizrachi L, Boise LH. Gene integrated set profile analysis: a context-based approach for inferring biological endpoints. Nucleic Acids Res. 2016 Apr 20;44(7):e69. doi: 10.1093/nar/gkv1503. Epub 2016 Jan 29. PubMed PMID: 26826710; PubMed Central PMCID: PMC4838358.