smfishHmrf

Release 1.3.3

HMRF for spatial transcriptomic data

Homepage PyPI

License
MIT
Install
pip install smfishHmrf==1.3.3

Documentation

smFish spatial pattern mining and cell type prediction

This package is organized into two components:

  1. smfishHmrf R package (directory: smfishHmrf)
  2. SVM prediction Python script (directory: svmPredict)

The components are independent (neither needs the other package to run). The third directory (hmrf-usage) contains important usage examples to help users get familiar with using the smfishHmrf R package for spatial pattern mining.

Installing smfishHmrf R package

to build:

tar -czf smfishHmrf.tar.gz smfishHmrf

to install:

R CMD INSTALL smfishHmrf.tar.gz

Prerequisites for SVM predictions

matplotlib, seaborn, pandas, numpy, scipy

If any of the above packages is missing, please install it using pip:

pip install <package name>

Or if you would like to install per user:

pip install --user <package name>

Note that the Python script is written in Python 2.7 and is incompatible with Python 3.

Running smfishHmrf

See hmrf-usage/README.md

Running cell type prediction

See svmPredict/README.md

Source data

See SOURCE_DATA.md

Stats

Dependencies
5
Dependent packages
0
Dependent repositories
0
Total releases
18
Latest release
First release
Forks
0
Watchers
1
Contributors
0
Repository size
8.86 MB
SourceRank
7

Development practices

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Releases

1.3.3
1.3.2
1.3.1
1.3.0
1.0.8.6
1.0.8.5
1.0.8.4
1.0.8.3
1.0.8.2
1.0.8.1
See all 18 releases

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