Metadata-Version: 2.1
Name: kb_python
Version: 0.24.2
Summary: Python wrapper around kallisto | bustools for scRNA-seq analysis
Home-page: https://github.com/pachterlab/kb_python
Author: Kyung Hoi (Joseph) Min
Author-email: phoenixter96@gmail.com
Maintainer: Pachter Lab
Maintainer-email: lsledd@caltech.edu
License: BSD
Description: # kb-python
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        kb-python is a python package that wraps the [kallisto | bustools](https://www.kallistobus.tools) single-cell RNA-seq workflow [1]. It was developed by Kyung Hoi (Joseph) Min and A. Sina Booeshaghi.
        
        The wrapper simplifies downloading and running of the kallisto
        [1] and bustools [2] programs. It was inspired by Sten Linnarsson’s `loompy
        fromfq` command (http://linnarssonlab.org/loompy/kallisto/index.html)
        
        The `kb` program consists of two parts:
        
        The `kb ref` command builds or downloads a species-specific index for
        pseudoalignment of reads. This command must be run prior to `kb count`, and it
        runs the `kallisto index` [1].
        
        The `kb count` command runs the kallisto [1] and bustools [2] programs. It can
        be used for pre-processing of data from a variety of single-cell RNA-seq
        technologies, and for a number of different workflows (e.g. production of gene
        count matrices, RNA velocity analyses, etc.). The output can be saved in a
        variety of formats including mtx and loom.
        
        If you use `kb` we ask that you cite the following two papers:
        
        [1] Bray, N. L., Pimentel, H., Melsted, P., & Pachter, L. (2016). Near-optimal
        probabilistic RNA-seq quantification. Nature biotechnology, 34(5), 525.
        
        [2] Melsted, P., Booeshaghi, A. S., Gao, F., da Veiga Beltrame, E., Lu, L.,
        Hjorleifsson, K. E., Gehring, J., & Pachter, L. (2019). Modular and efficient
        pre-processing of single-cell RNA-seq. BioRxiv, 673285.
        
        ## Prerequisites
        None. The kallisto and bustools binaries are included with the package.
        
        ## Getting Started
        Visit the [Getting Started](https://www.kallistobus.tools/kb_getting_started) page.
        
        ## Documentation
        - User documentation and tutorials are available [here](https://www.kallistobus.tools/tutorials).
        - Developer documentation is hosted on [Read the Docs](https://kb-python.readthedocs.io/en/latest/).
        
Keywords: kallisto bustools
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Utilities
Requires-Python: >=3.6
Description-Content-Type: text/markdown
