https://github.com/cbg-ethz/treemhn
Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees
Science Score: 23.0%
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Low similarity (10.3%) to scientific vocabulary
Repository
Joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees
Basic Info
- Host: GitHub
- Owner: cbg-ethz
- License: gpl-3.0
- Language: R
- Default Branch: main
- Homepage: https://github.com/cbg-ethz/TreeMHN
- Size: 258 MB
Statistics
- Stars: 6
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 1
Metadata Files
README.md
This R package implements the TreeMHN model for the joint inference of exclusivity patterns and recurrent trajectories from tumor mutation trees. (bioRxiv preprint)
Quick start
TreeMHN takes as input a set of independent tumor mutation trees containing a total number of n mutations. The format is a dataframe with five columns:
Patient_ID: IDs of patients, unique for each patient;Tree_ID: IDs of mutation trees, unique within each patient;Node_ID: IDs of each node in the tree, including the root node (with ID "1"), unique for each node;Mutation_ID: IDs of each mutational event. The root node has a mutation ID of "0", and other mutation IDs can be duplicated in the tree to allow for parallel mutations;Parent_ID: IDs of the parent node ID. The root node has itself as parent (ID "1").
The output is an n-by-n matrix representing the Mutual Hazard Network. The diagonal entries of this matrix indicate how often each mutation will occur and fixate independent of the other mutations. The off-diagonal entries encode the exclusivity and co-occurrence patterns of mutations. Conditioned on the estimated matrix, we can compute the probabilities of different evolutionary trajectories or evaluate the most likely next mutational events given a tumor tree.
Please see Demo.md for more details.
Installation
For Mac users, please compile the package with g++ instead of clang. To do this, you need to first install gcc using Homebrew:
brew install gcc
Then, create ~/.R/Makevars with entry
CXX=$(brew --prefix)/bin/g++-[INSTALLED VERSION]
For all users, install the devtools package in R and run
devtools::install_github("cbg-ethz/TreeMHN")
The installation typically takes around one minute to finish.
Owner
- Name: Computational Biology Group (CBG)
- Login: cbg-ethz
- Kind: organization
- Location: Basel, Switzerland
- Website: https://www.bsse.ethz.ch/cbg
- Twitter: cbg_ethz
- Repositories: 91
- Profile: https://github.com/cbg-ethz
Beerenwinkel Lab at ETH Zurich
GitHub Events
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Last Year
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Committers
Last synced: about 1 year ago
Top Committers
| Name | Commits | |
|---|---|---|
| Xiang Ge Luo | l****x@b****h | 60 |
| xgluo | 5****o | 37 |
| Xiang Ge Luo | l****x@b****h | 23 |
| Xiang Ge Luo | l****x@e****h | 2 |
| Xiang Ge Luo | l****x@e****h | 1 |
| Xiang Ge Luo | l****x@e****h | 1 |
Committer Domains (Top 20 + Academic)
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- Total pull requests: 1
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- Total pull request authors: 1
- Average comments per issue: 0
- Average comments per pull request: 0.0
- Merged pull requests: 1
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Dependencies
- DiagrammeR * imports
- Matrix * imports
- Rcpp * imports
- dplyr * imports
- ggm * imports
- ggplot2 * imports
- gridExtra * imports
- gtools * imports
- reshape2 * imports