################# Welcome to scipr! ################# .. image:: https://img.shields.io/pypi/v/scipr.svg :target: https://pypi.python.org/pypi/scipr .. image:: https://img.shields.io/travis/amiralavi/scipr.svg :target: https://travis-ci.com/amiralavi/scipr .. image:: https://readthedocs.org/projects/scipr/badge/?version=latest :target: https://scipr.readthedocs.io/en/latest/?badge=latest :alt: Documentation Status .. toctree:: :maxdepth: 3 :hidden: self intro installation api .. toctree:: :maxdepth: 2 :hidden: extending contributing .. toctree:: :maxdepth: 1 :hidden: authors .. toctree:: :maxdepth: 2 :hidden: history ************** What is scipr? ************** Single Cell Iterative Point set Registration (scipr) learns a transformation function to align batches of scRNA-seq data. This site covers scipr's usage & API documentation. *********** Quick start *********** Learn a function to align two batches of scRNA-seq data:: import scipr from scipr.matching import MNN from scipr.transform import Affine model = scipr.SCIPR(match_algo=MNN(), transform_algo=Affine()) model.fit(batch_A, batch_B) Apply the function to align data:: batch_A_aligned = model.transform(batch_A) ********** Learn more ********** Read more about how scipr works in the :ref:`get-started` guide. For documentation on each of the functions available in scipr, see the :ref:`api`. This package is based on the methods presented in our `PLOS Computational Biology paper `_. scipr is made available for free under a BSD license. **************** Related projects **************** ScRNA-seq alignment (or "batch correction") methods is an active area of developement. Here are just a few other related works you might be interested in: * `Seurat v3 `_ * `scAlign `_ * `Harmony `_ * `mnnpy `_ Indices and tables ================== * :ref:`genindex` * :ref:`search`