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Package for temporal deconvolution of bulk RNA-seq samples using SVI

License: BSD 3-Clause "New" or "Revised" License

Jupyter Notebook 97.75% Python 2.24% Makefile 0.01%

temporal-rna-seq-deconvolution's Introduction

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

git clone [email protected]:broadinstitute/temporal-rna-seq-deconvolution
cd temporal-rna-seq-deconvolution

In ubuntu you might need to install the following for the packages to compile

sudo apt-get install libglib2.0-dev python3-dev

Install python package

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:

CLI Use

ternadecov offers an cli for automated deconvolution and exporting of results from the command line. An example run call could be:

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: