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disc
pypi i disc
dis

disc

A highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning.

by Hao Yuan

1.1.6 (see all)License:Apache License 2.0
pypi i disc
Readme

DISC

|PyPI|

.. |PyPI| image:: https://img.shields.io/pypi/v/DISC.svg :target: https://pypi.org/project/disc

A highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning.

  • Free software: Apache License 2.0

Requirements

  • Python_ >=3.6
  • TensorFlow_ >=1.13.1,<2.0.0
  • numpy_ >=1.14.0
  • pandas_ >=0.21.0
  • h5py_ >=2.9.0
  • matplotlib_ >=3.0.0

Installation

  • Install TensorFlow

    If you have an Nvidia GPU, be sure to install a version of TensorFlow that supports it first -- DISC runs much faster with GPU::

    pip install "tensorflow-gpu>= 1.13.1,<2.0.0"

    We typically tensorflow-gpu==1.13.1.

    Here are requirements for GPU version TensorFlow_::

    • Hardware
      • NVIDIA GPU card with CUDA Compute Capability 3.5 or higher.
    • Software
      • NVIDIA GPU drivers - CUDA 10.0 requires 410.x or higher.
      • CUDA Toolkit - TensorFlow_ supports CUDA 10.0 (TensorFlow >= 1.13.0)
      • CUPTI ships with the CUDA Toolkit.
      • cuDNN SDK (>= 7.4.1)

    See this__ for further information.

    .. __: https://www.tensorflow.org/install/gpu

  • Install DISC with pip

    To install with pip, run the following from a terminal::

    pip install disc

  • Install DISC from GitHub

    To clone the repository and install manually, run the following from a terminal::

    git clone git://github.com/iyhaoo/DISC.git

    cd disc

    python setup.py install

Usage

References

Yao He:sup:#, Hao Yuan:sup:#, Cheng Wu:sup:#, Zhi Xie:sup:*. DISC: a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning. Genome Biology 21, 170 (2020). https://doi.org/10.1186/s13059-020-02083-3

History

1.1 (2020-06-06) ^^^^^^^^^^^^^^^^

  • Update CLI.

1.0 (2019-12-16) ^^^^^^^^^^^^^^^^^^

  • First release on PyPI_.

.. Python: https://www.python.org/downloads/ .. _TensorFlow: https://www.tensorflow.org/ .. _numpy: https://numpy.org/ .. _pandas: https://pandas.pydata.org/ .. _h5py: https://www.h5py.org/ .. _matplotlib: https://matplotlib.org/ .. hdf5-formatted: https://www.hdfgroup.org/solutions/hdf5/ .. Data availability: https://github.com/iyhaoo/DISC_data_availability/ .. loom-formatted: http://loompy.org/ .. pb: https://www.tensorflow.org/guide/saved_model/ .. RDS-formatted: https://stat.ethz.ch/R-manual/R-devel/library/base/html/readRDS.html .. _Run imputation: https://github.com/iyhaoo/DISC/blob/master/reproducibility/data_preparation_and_imputation/run_imputation.md .. _PyPI: https://pypi.org/project/disc/

GitHub Stars

10

LAST COMMIT

1yr ago

MAINTAINERS

1

CONTRIBUTORS

3

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0

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VersionTagPublished
1.1.6
1yr ago
1.1.2
2yrs ago
1.1.1
2yrs ago
1.1.0
2yrs ago
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