Resources
Software
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CliPP/CSR
CliPP/CSR Clonal structure identification through penalizing pairwise differences. Consensus Clustering for Subclonal s
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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. You may read more about setting up the conda environment here.
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
Tutorials for running deconvolution
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
- How to improve scientific writing, by Xiaoqian Liu