Skip to main content

SpaDecon: cell-type deconvolution in spatial transcriptomics with semi-supervised learning

Project description

SpaDecon: cell-type deconvolution in spatial transcriptomics with semi-supervised learning

Kyle Coleman, Jian Hu, Amelia Schroeder, Edward B. Lee, Mingyao Li*

SpaDecon is a semi-supervised learning-based method developed to perform cell-type deconvolution on spatially resolved transcriptomics (SRT) datasets. SpaDecon has been shown to provide accurate cell-type deconvolution results for both Spatial Transcriptomics (ST) and 10X Visium SRT datasets. Annotated scRNA-seq gene expression data from the same type of tissue as the SRT data are required for deconvolution.

png

SpaDecon Installation

  • SpaDecon installation requires a python version of at least 3.6. The version of python can be checked by:
import platform
platform.python_version()
'3.7.11'

We recommend creating and activating a new conda environment when installing the SpaDecon package. For instance,

conda create -n SpaDecon python=3.7
conda activate SpaDecon

There are mulitple ways to install SpaDecon:

  • Install SpaDecon using PyPI:
pip3 install SpaDecon   
  • Download and install SpaDecon package from GitHub:
git clone https://github.com/kpcoleman/SpaDecon
cd SpaDecon/
python3 setup.py install --user

Tutorial

A markdown tutorial file can be found here: https://github.com/kpcoleman/SpaDecon/blob/main/tutorial/Tutorial.md

A tutorial in the form of a jupyter notebook can be found here: https://github.com/kpcoleman/SpaDecon/blob/main/tutorial/tutorial.ipynb

Software Requirements

python >= 3.6
keras==2.2.4
pandas==1.2.4
numpy==1.20.1
scipy==1.6.2
scanpy==1.7.0
anndata==0.7.6
sklearn
tensorflow==1.14.0

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

SpaDecon-1.1.2.tar.gz (18.5 kB view details)

Uploaded Source

Built Distribution

SpaDecon-1.1.2-py3-none-any.whl (20.7 kB view details)

Uploaded Python 3

File details

Details for the file SpaDecon-1.1.2.tar.gz.

File metadata

  • Download URL: SpaDecon-1.1.2.tar.gz
  • Upload date:
  • Size: 18.5 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.7.4

File hashes

Hashes for SpaDecon-1.1.2.tar.gz
Algorithm Hash digest
SHA256 38c17cc1ef206628a01d5c2f29cd04c2e07a7c6a8a97d48f82c2d66bc392c44b
MD5 46c5b3bccb52c2fb76c55aaa757479ec
BLAKE2b-256 faa096e2f8fba0e577948f7e7e948f31aa619968bd1ce0861f94ff392c341826

See more details on using hashes here.

File details

Details for the file SpaDecon-1.1.2-py3-none-any.whl.

File metadata

  • Download URL: SpaDecon-1.1.2-py3-none-any.whl
  • Upload date:
  • Size: 20.7 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/4.0.2 CPython/3.7.4

File hashes

Hashes for SpaDecon-1.1.2-py3-none-any.whl
Algorithm Hash digest
SHA256 b418db83b1b43f9dbc374ff0b4a59e1a809b870790788ca023c842a06a20dd6b
MD5 84509b0a3cb360b8249fbe0853bfae65
BLAKE2b-256 3f35388a969c51e8552f40f5c081a845b8f8a722ec8f0d245bc8026e2ee1ebe5

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page