Resources
Software
Tutorials
Using Conda to manage R/Python environments and packages
We recommend using conda to manage R/Python environments and packages either on personal computers or on servers and clusters. You can also use conda to install softwares such as samtools. This is particularly useful when we are non-root users, which often prevents us from setting up the right computing environment. For a copy of instructions and tips on setting up the conda environment, please email Dr. Wang.
Resources for single cell RNA-seq data analysis
TmS
Computational packages for single cell analysis
A comprehensive list of single cell resources
Single cell workshops
Technical solutions
For a copy of any of the following instructions, please email Dr. Wang.
- Use SRA toolkit to download sequencing data for CellRanger
- Build R & Python environment on remote servers using Jupyter notebook
- Troubleshooting for RStudio: run RStudio in your own R environment
Tutorials for running deconvolution
For a copy of any of the following tutorials, please email Dr. Wang.
- Tutorial for running DeMixT and TmS
- Tutorial for running DeMixNB
Statistics/machine learning tutorials
For a copy of any of the following tutorials, please email Dr. Wang.
- Feature Selection: Variable selection & model selection, by Xiaoqian Liu
- R's C interface tutorial, by Xiaoqian Liu
- Feature Selection II, by Xiaoqian Liu
Scientific writing tutorials
For a copy of any of the, "How to improve scientific writing" tutorial by Xiaoqian Liu, please email Dr. Wang.
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