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
deconvolution pyro rna-seq single-cell-rna-seq svi transcriptomics
Last synced: 8 months ago
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Package for temporal deconvolution of bulk RNA-seq samples using SVI
- Host: GitHub
- URL: https://github.com/broadinstitute/temporal-rna-seq-deconvolution
- Owner: broadinstitute
- License: bsd-3-clause
- Created: 2021-04-07T22:36:19.000Z (over 4 years ago)
- Default Branch: main
- Last Pushed: 2023-10-05T19:36:49.000Z (about 2 years ago)
- Last Synced: 2024-12-31T19:53:28.519Z (9 months ago)
- Topics: deconvolution, pyro, rna-seq, single-cell-rna-seq, svi, transcriptomics
- Language: Jupyter Notebook
- Homepage: https://ternadecov.readthedocs.io/en/latest/source/ternadecov.html
- Size: 22.1 MB
- Stars: 1
- Watchers: 4
- Forks: 0
- Open Issues: 7
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# 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](https://ternadecov.readthedocs.io/en/latest/source/ternadecov.html).
## Tutorials
For a full tutorial on the use of ternadecov please visit the [GP deconvolution tutorial](notebooks/tutorials/tutorial-deconvolve-gp.ipynb).
Additional tutorials provide information on:
* [Simulating and saving datasets](notebooks/tutorials/tutorial-simulate-save.ipynb)
* [Simulating linear trajectories](notebooks/tutorials/tutorial-deconvolve-simulated-linear.ipynb)
* [Simulating sigmoid trajectories](notebooks/tutorials/tutorial-deconvolve-simulated-sigmoid.ipynb)
* [Simulating periodic trajectories](notebooks/tutorials/tutorial-deconvolve-simulated-periodic.ipynb)
* [Evaluating the time required to run the deconvolution for different numbers of samples](notebooks/tutorials/tutorial-evaluate-run-time-gp.ipynb)
## 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 dpi_time \
--feature-selection-method overdispersed_bulk_and_high_sc \
--export-prefix results_ \
--export-directory output/
```
For more information on CLI usage try:
```bash
ternadecov --help
```