Artemether_scRNA

Single cell RNA-seq analysis of pancreatic islets with drug treatment. This is the code used to analyze this dataset.

Structure

Scripts to analyze all data are in src/, see the readme file in this directory for more details. Additional data (i.e. list of marker genes, etc) are in the folder metadata/.

System requirements

The code provided requires the setting of two environmental variables $CODEBASE (where the code is) and $PROCESSED (where the data is and analysis results will be stored). For example:

export CODEBASE="$HOME/code/"
export PROCESSED="$HOME/projects/"

Genome alignments are based on CellRanger (version 2.1.0). Statistical analysis is based on R (version 3.4.0), using the following packages:

• SoupX (version 0.1.1)
• Seurat (version 2.0.1)
• cowplot (version 0.8.0)
• Rtsne (version 0.13)
• ROCR (version 1.0-7)
• gplots (version 3.0.1.1)
• rhdf5 (version 2.20.0)
• pryr (version 0.1.4)
• project.init (version 0.0.1)
• pheatmap (version 1.0.12)
• glmnet (version 2.0-18)
• enrichR (version 1.0)
• dplyr (version 0.7.2)
• doMC (version 1.3.4)
• iterators (version 1.0.12)
• foreach (version 1.4.3)
• data.table (version 1.12.2)
• cellrangerRkit (version 2.0.0)
• Rmisc (version 1.5)
• plyr (version 1.8.4)
• lattice (version 0.20-38)
• ggplot2 (version 3.1.1)
• RColorBrewer (version 1.1-2)
• Matrix (version 1.2-17)