You will need some R packages, gplots and plotrix, these can be installed with the command:Īll the commands that are run in this example can also be found in the file: run_PCA_clust.R Data processingįirst read in the data and define colors/symbols for plotting proj/b2013006/webexport/downloads/courses/RNAseqWorkshop/pca_clustĬopy all that data to your folder of choice (on uppmax or your own computer) and start R in that folder. 193-196, “Single-Cell RNA-Seq Reveals Dynamic, Random Monoallelic Gene Expression in Mammalian Cells”Īll data you need is available in the folder: The dataset used is single-cell RNA-seq data from mouse embryonic development from Deng. These methods can also be applied to any other type of dataset, such as RNA-seq or other high throuput data. Here are some examples on how to run PCA/Clustering on a single cell RNA-seq dataset. PCA and clustering on a single cell RNA-seq dataset
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