tsteelejohnson91 / DEGAS

DEGAS is an R package that can be used to prioritize cells in relation to disease.

Diagnostic Evidence GAuge of Single cells (DEGAS): A flexible deep transfer learning framework for prioritizing cells in relation to disease

https://doi.org/10.1186/s13073-022-01012-2

Package development by:
Zhi Huang (https://github.com/huangzhii)
Travis S. Johnson (https://github.com/tsteelejohnson91)

Installation

• Step 1 Install python3 and pip3 if not previously installed
  • https://wiki.python.org/moin/BeginnersGuide/Download
  • https://www.python.org/downloads/
• Step 2 Install python packages from terminal

pip3 install tensorflow
pip3 install functools
pip3 install numpy
pip3 install math

• Step 3 Install devtools in R

install.packages("devtools")

• Step 4 Install DEGAS in R

library(devtools)
install_github("tsteelejohnson91/DEGAS")

• Step 5 Install packages useful for downstream analysis in R

install.packages("Rtsne")
install.packages("ggplot2")

Prerequisites

OS

• OSX
• Linux

Python packages

• tensorflow
• functools
• numpy
• math

R

• Rtsne
• ggplot2

Configurations tested

Mac CPU

• R (4.0.1), Python (3.8.2), TensorFlow (2.3.1), NumPy (1.18.5), functools (3.8.2), math (3.8.2)
• R (4.1.0), Python (3.8.3), TensorFlow (2.5.0), NumPy (1.19.5), functools (3.8.3), math (3.8.3)
• R (3.5.1), Python (3.6.0), TensorFlow (2.3.1), NumPy (1.17.4), functools (3.6.0), math (3.6.0)

Linux GPU

• R (3.4.4), Python (anaconda 3.6.5), TensorFlow GPU-enabled (1.9.0), NumPy (1.14.3), functools (anaconda 3.6.5), math (anaconda 3.6.5)

R Package Versions

• Rtsne: 0.15,
• ggplot2: 3.3.5, 3.3.0, 3.2.1
• See Session Info in the Simulation, GBM, AD, and MM examples for more version details
  • e.g. See bottom of https://github.com/tsteelejohnson91/DEGAS/blob/master/MM_example/MM_example.md

Python package versions

• TensorFlow: 2.3.1, 2.5.0, 2.3.1, 1.9.0 (GPU)
• Numpy: 1.18.5, 1.19.5, 1.17.4, 1.14.3
• functools: 3.8.2, 3.8.3, 3.6.0, anaconda 3.6.5
• math: 3.8.2, 3.8.3, 3.6.0, anaconda 3.6.5

DEGAS documentation and examples

• Documentation (https://github.com/tsteelejohnson91/DEGAS/blob/master/DEGAS_documentation.md)
• Simulation example (https://github.com/tsteelejohnson91/DEGAS/blob/master/Sim_example/Sim_example.md)
• GBM example (https://github.com/tsteelejohnson91/DEGAS/blob/master/GBM_example/GBM_example.md)
• AD example (https://github.com/tsteelejohnson91/DEGAS/blob/master/AD_example/AD_example.md)
• MM example (https://github.com/tsteelejohnson91/DEGAS/blob/master/MM_example/MM_example.md)
• BRCA spatial transcriptomics example (https://github.com/tsteelejohnson91/DEGAS/blob/master/BRCA_ST_example/BRCA_ST_example.md)

Coming Soon

Diagnostic Evidence GAuge of Spatial transcriptomics (DEGAS)

Usage tracking

Please click this link to help us track our usage. https://tsteelejohnson91.github.io/DEGAS/