https://github.com/broadinstitute/temporal-rna-seq-deconvolution
Package for temporal deconvolution of bulk RNA-seq samples using SVI
https://github.com/broadinstitute/temporal-rna-seq-deconvolution
Science Score: 26.0%
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Low similarity (11.9%) to scientific vocabulary
Keywords
Repository
Package for temporal deconvolution of bulk RNA-seq samples using SVI
Basic Info
- Host: GitHub
- Owner: broadinstitute
- License: bsd-3-clause
- Language: Jupyter Notebook
- Default Branch: main
- Homepage: https://ternadecov.readthedocs.io/en/latest/source/ternadecov.html
- Size: 22.1 MB
Statistics
- Stars: 2
- Watchers: 3
- Forks: 0
- Open Issues: 7
- Releases: 0
Topics
Metadata Files
README.md
Temporal RNA-seq Deconvolution (TeRNAdecov)
TeRNAdecov is a package for deconvolution of bulk RNA-seq samples from time series using single-cell datasets. It allows for simultaneous inference of sample-specific composition as well as overall time trajectory dynamics using highly scalable stochastic variational inference.
Install
Installation in an Anaconda environment is recommended.
Install pyro (https://pyro.ai/) and pytorch
Clone the repository
sh
git clone git@github.com:broadinstitute/temporal-rna-seq-deconvolution
cd temporal-rna-seq-deconvolution
In ubuntu you might need to install the following for the packages to compile
sh
sudo apt-get install libglib2.0-dev python3-dev
Install python package
py
pip install -e .
Documentation
Auto-generated code documentation for the package can be found on readthedocs.io.
Tutorials
For a full tutorial on the use of ternadecov please visit the GP deconvolution tutorial.
Additional tutorials provide information on: * Simulating and saving datasets * Simulating linear trajectories * Simulating sigmoid trajectories * Simulating periodic trajectories * Evaluating the time required to run the deconvolution for different numbers of samples
CLI Use
ternadecov offers an cli for automated deconvolution and exporting of results from the command line. An example run call could be:
```bash
ternadecov deconvolve \ --bulk-anndata bulk.h5ad \ --sc-anndata singlecell.h5ad \ --iterations 20000 \ --sc-celltype-column Abbreviation \ --bulk-time-column dpitime \ --feature-selection-method overdispersedbulkandhighsc \ --export-prefix results \ --export-directory output/ ```
For more information on CLI usage try:
bash
ternadecov --help
Owner
- Name: Broad Institute
- Login: broadinstitute
- Kind: organization
- Location: Cambridge, MA
- Website: http://www.broadinstitute.org/
- Twitter: broadinstitute
- Repositories: 1,083
- Profile: https://github.com/broadinstitute
Broad Institute of MIT and Harvard
GitHub Events
Total
Last Year
Issues and Pull Requests
Last synced: 9 months ago
All Time
- Total issues: 12
- Total pull requests: 2
- Average time to close issues: 1 day
- Average time to close pull requests: 1 day
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 0.0
- Average comments per pull request: 0.0
- Merged pull requests: 2
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- barkasn (8)
Pull Request Authors
- barkasn (2)
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Dependencies
- for *
- line.rstrip *
- os.path.join *