https://github.com/soedinglab/csgraph_mod
Modification of the scipy csgraph class to allow tracking of the visited nodes
https://github.com/soedinglab/csgraph_mod
Last synced: 12 months ago
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Modification of the scipy csgraph class to allow tracking of the visited nodes
- Host: GitHub
- URL: https://github.com/soedinglab/csgraph_mod
- Owner: soedinglab
- License: other
- Created: 2016-10-24T13:28:03.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2019-08-02T14:16:13.000Z (almost 7 years ago)
- Last Synced: 2025-01-09T06:51:22.875Z (over 1 year ago)
- Language: Python
- Homepage:
- Size: 1.37 MB
- Stars: 0
- Watchers: 6
- Forks: 1
- Open Issues: 0
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Metadata Files:
- Readme: README.md
- License: LICENSE.txt
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README
### `csgraph_mod`
We have modified the implementation of Dijkstra's algorithm contained in the [csgraph](https://docs.scipy.org/doc/scipy/reference/sparse.csgraph.html) module for compressed sparse graph routines to return a list of visited nodes. We use this package to help us construct a minimal spanning tree between single-cell transcriptomes. For more information about this, please refer to the [MERLoT manuscript](https://www.biorxiv.org/content/early/2018/02/08/261768).
### Installation
`csgraph_mod` can be installed using the `pip` package manager or any `pip`-compatible package manager:
git clone https://github.com/soedinglab/csgraph_mod.git
cd csgraph_mod/
pip install .
### Dependencies
`csgraph_mod` was developed and tested in [Python 3.5](https://www.python.org/downloads/release/python-350/) and [3.6](https://www.python.org/downloads/release/python-360/). While older Python 3 versions should work, there is no guarantee that they will. Installation requires:
* [`numpy`](www.numpy.org)
* [`scipy`](https://www.scipy.org/)
* [`cython`](http://cython.org/)
### Known problems
#### Missing `numpy` headers
In some cases (especially on Mac computers), the installer may complain that it cannot find some `numpy` headers:
fatal error: 'numpy/arrayobject.h' file not found
In this case, try exporting the headers yourself. Run `export CFLAGS="-I /site-packages/numpy/core/include $CFLAGS"`, where `` is the directory where python is installed - something like `/usr/local/lib/python3.6`.