From 86cfef55fbf08dc1885a52ec3082ed9f7cca6d03 Mon Sep 17 00:00:00 2001
From: Praneet Chaturvedi <55851416+praneet1988@users.noreply.github.com>
Date: Tue, 15 Sep 2020 17:25:57 -0400
Subject: [PATCH] Add files via upload

---
 install_R_packages.R | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 install_R_packages.R

diff --git a/install_R_packages.R b/install_R_packages.R
new file mode 100644
index 0000000..62f7012
--- /dev/null
+++ b/install_R_packages.R
@@ -0,0 +1,31 @@
+options(repos = BiocManager::repositories())
+if (!require("devtools")) install.packages("devtools", repos="http://cran.us.r-project.org")
+if (!require("shiny")) install.packages("shiny", repos="http://cran.us.r-project.org")
+if (!require("servr")) install.packages("servr", repos="http://cran.us.r-project.org")
+if (!require("ggplot2")) install.packages("ggplot2", repos="http://cran.us.r-project.org")
+if (!require("pheatmap")) install.packages("pheatmap", repos="http://cran.us.r-project.org")
+if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")
+if (!require("M3C")) BiocManager::install("M3C")
+if (!require("RUVSeq")) BiocManager::install("RUVSeq")
+if (!require("scales")) install.packages("scales", repos="http://cran.us.r-project.org")
+if (!require("dtwclust")) install.packages("dtwclust", repos="http://cran.us.r-project.org")
+if (!require("dplyr")) install.packages("dplyr", repos="http://cran.us.r-project.org")
+if (!require("DESeq2")) BiocManager::install("DESeq2")
+if (!require("ggcorrplot")) install.packages("ggcorrplot", repos="http://cran.us.r-project.org")
+if (!require("tibble")) install.packages("tibble", repos="http://cran.us.r-project.org")
+if (!require("ReactomePA")) BiocManager::install("ReactomePA")
+if (!require("org.Hs.eg.db")) BiocManager::install("org.Hs.eg.db")
+if (!require("org.Mm.eg.db")) BiocManager::install("org.Mm.eg.db")
+if (!require("AnnotationDbi")) BiocManager::install("AnnotationDbi")
+if (!require("EnhancedVolcano")) BiocManager::install("EnhancedVolcano")
+if (!require("ChIPseeker")) BiocManager::install("ChIPseeker")
+if (!require("TxDb.Hsapiens.UCSC.hg19.knownGene")) BiocManager::install("TxDb.Hsapiens.UCSC.hg19.knownGene")
+if (!require("TxDb.Mmusculus.UCSC.mm10.knownGene")) BiocManager::install("TxDb.Mmusculus.UCSC.mm10.knownGene")
+if (!require("TxDb.Hsapiens.UCSC.hg38.knownGene")) BiocManager::install("TxDb.Hsapiens.UCSC.hg38.knownGene")
+if (!require("TxDb.Mmusculus.UCSC.mm9.knownGene")) BiocManager::install("TxDb.Mmusculus.UCSC.mm9.knownGene")
+if (!require("clusterProfiler")) BiocManager::install("clusterProfiler")
+if (!require("cowplot")) install.packages("cowplot", repos="http://cran.us.r-project.org")
+if (!require("scater")) BiocManager::install("scater")
+if (!require("hdf5r")) install.packages("hdf5r", repos="http://cran.us.r-project.org")
+if (!require("MAST")) BiocManager::install("MAST")
+if (!require("Seurat")) install.packages("Seurat", repos="http://cran.us.r-project.org")
\ No newline at end of file