Resources
Software
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CliPP/CSR
Clonal structure ID through penalizing pairwise differences/Consensus clustering for subclonal structure reconstruction
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Famdenovo
An algorithm that calculates the probability of a germline mutation to be de novo based on family history data
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LFSPRO
Personalized risk assessment for families with Li-Fraumeni Syndrome (R package)
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SRMA
Sequence Robust Multi-array Analysis for resequencing arrays (R package)
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DeMixT
Software package that performs deconvolution on transcriptome data from a mixture of two or three components
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FamSeq
A C++ based software for variant calling in data generated from family-based sequencing studies
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MuSE
Mutation somatic evolution estimation for mutation calling in sequencing data of tumor-normal pair samples (C++)
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BayesMendel
A comprehensive environment for prediction of inherited cancer susceptibility (R package)
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
- 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
- Tutorial for running DeMixT and TmS
- Tutorial for running DeMixNB
Statistics/machine learning tutorials
- 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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Research Areas
Find out about the four types of research taking place at UT MD Anderson.