Metadata-Version: 2.1
Name: rnanorm
Version: 2.0.1
Summary: Common RNA-seq normalization methods
Author: Genialis, Inc.
Author-email: dev-team@genialis.com
License: 
                                         Apache License
                                   Version 2.0, January 2004
                                http://www.apache.org/licenses/
        
           TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
        
           1. Definitions.
        
              "License" shall mean the terms and conditions for use, reproduction,
              and distribution as defined by Sections 1 through 9 of this document.
        
              "Licensor" shall mean the copyright owner or entity authorized by
              the copyright owner that is granting the License.
        
              "Legal Entity" shall mean the union of the acting entity and all
              other entities that control, are controlled by, or are under common
              control with that entity. For the purposes of this definition,
              "control" means (i) the power, direct or indirect, to cause the
              direction or management of such entity, whether by contract or
              otherwise, or (ii) ownership of fifty percent (50%) or more of the
              outstanding shares, or (iii) beneficial ownership of such entity.
        
              "You" (or "Your") shall mean an individual or Legal Entity
              exercising permissions granted by this License.
        
              "Source" form shall mean the preferred form for making modifications,
              including but not limited to software source code, documentation
              source, and configuration files.
        
              "Object" form shall mean any form resulting from mechanical
              transformation or translation of a Source form, including but
              not limited to compiled object code, generated documentation,
              and conversions to other media types.
        
              "Work" shall mean the work of authorship, whether in Source or
              Object form, made available under the License, as indicated by a
              copyright notice that is included in or attached to the work
              (an example is provided in the Appendix below).
        
              "Derivative Works" shall mean any work, whether in Source or Object
              form, that is based on (or derived from) the Work and for which the
              editorial revisions, annotations, elaborations, or other modifications
              represent, as a whole, an original work of authorship. For the purposes
              of this License, Derivative Works shall not include works that remain
              separable from, or merely link (or bind by name) to the interfaces of,
              the Work and Derivative Works thereof.
        
              "Contribution" shall mean any work of authorship, including
              the original version of the Work and any modifications or additions
              to that Work or Derivative Works thereof, that is intentionally
              submitted to Licensor for inclusion in the Work by the copyright owner
              or by an individual or Legal Entity authorized to submit on behalf of
              the copyright owner. For the purposes of this definition, "submitted"
              means any form of electronic, verbal, or written communication sent
              to the Licensor or its representatives, including but not limited to
              communication on electronic mailing lists, source code control systems,
              and issue tracking systems that are managed by, or on behalf of, the
              Licensor for the purpose of discussing and improving the Work, but
              excluding communication that is conspicuously marked or otherwise
              designated in writing by the copyright owner as "Not a Contribution."
        
              "Contributor" shall mean Licensor and any individual or Legal Entity
              on behalf of whom a Contribution has been received by Licensor and
              subsequently incorporated within the Work.
        
           2. Grant of Copyright License. Subject to the terms and conditions of
              this License, each Contributor hereby grants to You a perpetual,
              worldwide, non-exclusive, no-charge, royalty-free, irrevocable
              copyright license to reproduce, prepare Derivative Works of,
              publicly display, publicly perform, sublicense, and distribute the
              Work and such Derivative Works in Source or Object form.
        
           3. Grant of Patent License. Subject to the terms and conditions of
              this License, each Contributor hereby grants to You a perpetual,
              worldwide, non-exclusive, no-charge, royalty-free, irrevocable
              (except as stated in this section) patent license to make, have made,
              use, offer to sell, sell, import, and otherwise transfer the Work,
              where such license applies only to those patent claims licensable
              by such Contributor that are necessarily infringed by their
              Contribution(s) alone or by combination of their Contribution(s)
              with the Work to which such Contribution(s) was submitted. If You
              institute patent litigation against any entity (including a
              cross-claim or counterclaim in a lawsuit) alleging that the Work
              or a Contribution incorporated within the Work constitutes direct
              or contributory patent infringement, then any patent licenses
              granted to You under this License for that Work shall terminate
              as of the date such litigation is filed.
        
           4. Redistribution. You may reproduce and distribute copies of the
              Work or Derivative Works thereof in any medium, with or without
              modifications, and in Source or Object form, provided that You
              meet the following conditions:
        
              (a) You must give any other recipients of the Work or
                  Derivative Works a copy of this License; and
        
              (b) You must cause any modified files to carry prominent notices
                  stating that You changed the files; and
        
              (c) You must retain, in the Source form of any Derivative Works
                  that You distribute, all copyright, patent, trademark, and
                  attribution notices from the Source form of the Work,
                  excluding those notices that do not pertain to any part of
                  the Derivative Works; and
        
              (d) If the Work includes a "NOTICE" text file as part of its
                  distribution, then any Derivative Works that You distribute must
                  include a readable copy of the attribution notices contained
                  within such NOTICE file, excluding those notices that do not
                  pertain to any part of the Derivative Works, in at least one
                  of the following places: within a NOTICE text file distributed
                  as part of the Derivative Works; within the Source form or
                  documentation, if provided along with the Derivative Works; or,
                  within a display generated by the Derivative Works, if and
                  wherever such third-party notices normally appear. The contents
                  of the NOTICE file are for informational purposes only and
                  do not modify the License. You may add Your own attribution
                  notices within Derivative Works that You distribute, alongside
                  or as an addendum to the NOTICE text from the Work, provided
                  that such additional attribution notices cannot be construed
                  as modifying the License.
        
              You may add Your own copyright statement to Your modifications and
              may provide additional or different license terms and conditions
              for use, reproduction, or distribution of Your modifications, or
              for any such Derivative Works as a whole, provided Your use,
              reproduction, and distribution of the Work otherwise complies with
              the conditions stated in this License.
        
           5. Submission of Contributions. Unless You explicitly state otherwise,
              any Contribution intentionally submitted for inclusion in the Work
              by You to the Licensor shall be under the terms and conditions of
              this License, without any additional terms or conditions.
              Notwithstanding the above, nothing herein shall supersede or modify
              the terms of any separate license agreement you may have executed
              with Licensor regarding such Contributions.
        
           6. Trademarks. This License does not grant permission to use the trade
              names, trademarks, service marks, or product names of the Licensor,
              except as required for reasonable and customary use in describing the
              origin of the Work and reproducing the content of the NOTICE file.
        
           7. Disclaimer of Warranty. Unless required by applicable law or
              agreed to in writing, Licensor provides the Work (and each
              Contributor provides its Contributions) on an "AS IS" BASIS,
              WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
              implied, including, without limitation, any warranties or conditions
              of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
              PARTICULAR PURPOSE. You are solely responsible for determining the
              appropriateness of using or redistributing the Work and assume any
              risks associated with Your exercise of permissions under this License.
        
           8. Limitation of Liability. In no event and under no legal theory,
              whether in tort (including negligence), contract, or otherwise,
              unless required by applicable law (such as deliberate and grossly
              negligent acts) or agreed to in writing, shall any Contributor be
              liable to You for damages, including any direct, indirect, special,
              incidental, or consequential damages of any character arising as a
              result of this License or out of the use or inability to use the
              Work (including but not limited to damages for loss of goodwill,
              work stoppage, computer failure or malfunction, or any and all
              other commercial damages or losses), even if such Contributor
              has been advised of the possibility of such damages.
        
           9. Accepting Warranty or Additional Liability. While redistributing
              the Work or Derivative Works thereof, You may choose to offer,
              and charge a fee for, acceptance of support, warranty, indemnity,
              or other liability obligations and/or rights consistent with this
              License. However, in accepting such obligations, You may act only
              on Your own behalf and on Your sole responsibility, not on behalf
              of any other Contributor, and only if You agree to indemnify,
              defend, and hold each Contributor harmless for any liability
              incurred by, or claims asserted against, such Contributor by reason
              of your accepting any such warranty or additional liability.
        
           END OF TERMS AND CONDITIONS
        
           APPENDIX: How to apply the Apache License to your work.
        
              To apply the Apache License to your work, attach the following
              boilerplate notice, with the fields enclosed by brackets "[]"
              replaced with your own identifying information. (Don't include
              the brackets!)  The text should be enclosed in the appropriate
              comment syntax for the file format. We also recommend that a
              file or class name and description of purpose be included on the
              same "printed page" as the copyright notice for easier
              identification within third-party archives.
        
           Copyright [yyyy] [name of copyright owner]
        
           Licensed under the Apache License, Version 2.0 (the "License");
           you may not use this file except in compliance with the License.
           You may obtain a copy of the License at
        
               http://www.apache.org/licenses/LICENSE-2.0
        
           Unless required by applicable law or agreed to in writing, software
           distributed under the License is distributed on an "AS IS" BASIS,
           WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
           See the License for the specific language governing permissions and
           limitations under the License.
        
Project-URL: repository, https://github.com/genialis/RNAnorm
Keywords: bio,bioinformatics,data science,machine learning,artificial intelligence,python,genialis,rnaseq,normalization
Classifier: Development Status :: 5 - Production/Stable
Classifier: Environment :: Console
Classifier: Intended Audience :: Developers
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Requires-Python: <3.12,>=3.8
Description-Content-Type: text/x-rst
License-File: LICENSE
Requires-Dist: click
Requires-Dist: numpy>=1.0.0
Requires-Dist: pandas>=1.0.0
Requires-Dist: scikit-learn>=1.0.0
Requires-Dist: pandera
Provides-Extra: docs
Requires-Dist: sphinx>=5.1.1; extra == "docs"
Requires-Dist: sphinx-autodoc-typehints>=1.19.2; extra == "docs"
Provides-Extra: package
Requires-Dist: build>=0.8.0; extra == "package"
Requires-Dist: check-manifest>=0.48; extra == "package"
Requires-Dist: twine>=4.0.1; extra == "package"
Provides-Extra: test
Requires-Dist: black; extra == "test"
Requires-Dist: flake8; extra == "test"
Requires-Dist: isort; extra == "test"
Requires-Dist: mypy; extra == "test"
Requires-Dist: pydocstyle[toml]; extra == "test"
Requires-Dist: pytest; extra == "test"
Requires-Dist: pytest-cov; extra == "test"

====================================
RNA-seq data normalization in Python
====================================

|build| |black| |docs| |pypi_version| |pypi_pyversions| |pypi_downloads|

.. |build| image:: https://github.com/genialis/RNAnorm/actions/workflows/build.yml/badge.svg?branch=main
    :target: https://github.com/genialis/RNAnorm/actions?query=branch%3Amain
    :alt: Build Status

.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
    :target: https://github.com/psf/black
    :alt: Code Style Black

.. |docs| image:: https://readthedocs.org/projects/rnanorm/badge/?version=latest
    :target: http://rnanorm.readthedocs.io/
    :alt: Documentation Status

.. |pypi_version| image:: https://img.shields.io/pypi/v/rnanorm.svg
    :target: https://pypi.org/project/rnanorm
    :alt: Version on PyPI

.. |pypi_pyversions| image:: https://img.shields.io/pypi/pyversions/rnanorm.svg
    :target: https://pypi.org/project/rnanorm
    :alt: Supported Python versions

.. |pypi_downloads| image:: https://pepy.tech/badge/rnanorm
    :target: https://pepy.tech/project/rnanorm
    :alt: Number of downloads from PyPI


Python implementation of common RNA-seq normalization methods:

- CPM (Counts per million)
- FPKM_ (Fragments per kilobase million)
- TPM_ (Transcripts per million)
- UQ_ (Upper quartile)
- CUF_ (Counts adjusted with UQ factors)
- TMM_ (Trimmed mean of M-values)
- CTF_ (Counts adjusted with TMM factors)

For in-depth description of methods see documentation_.

.. _FPKM: https://www.nature.com/articles/nmeth.1226
.. _TPM: https://link.springer.com/article/10.1007/s12064-012-0162-3
.. _UQ: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-94
.. _CUF: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02568-9/
.. _TMM: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-3-r25
.. _CTF: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02568-9/
.. _documentation: https://rnanorm.readthedocs.io/


Features
========

- Pure Python implementation (no need for R, etc.)
- Compatible with Scikit-learn_
- Command line interface
- Verbose documentation_
- Validated method implementation


.. _Scikit-learn: https://scikit-learn.org/
.. _documentation: https://rnanorm.readthedocs.io/


Install
=======

We recommend installing RNAnorm with pip::

   pip install rnanorm


Quick start
===========

The implemented methods can be executed from Python or from the command line.

Normalize from Python
---------------------

The most common use case is to run normalization from Python::

   >>> from rnanorm.datasets import load_toy_data
   >>> from rnanorm import FPKM
   >>> dataset = load_toy_data()
   >>> # Expressions need to have genes in columns and samples in rows
   >>> dataset.exp
             Gene_1  Gene_2  Gene_3  Gene_4  Gene_5
   Sample_1     200     300     500    2000    7000
   Sample_2     400     600    1000    4000   14000
   Sample_3     200     300     500    2000   17000
   Sample_4     200     300     500    2000    2000
   >>> fpkm = FPKM(dataset.gtf_path).set_output(transform="pandas")
   >>> fpkm.fit_transform(dataset.exp)
                Gene_1    Gene_2    Gene_3    Gene_4    Gene_5
   Sample_1   100000.0  100000.0  100000.0  200000.0  700000.0
   Sample_2   100000.0  100000.0  100000.0  200000.0  700000.0
   Sample_3    50000.0   50000.0   50000.0  100000.0  850000.0
   Sample_4   200000.0  200000.0  200000.0  400000.0  400000.0


Normalize from command line
---------------------------

Normalization from the command line is also supported. To list available
methods and general help::

    rnanorm --help

Get info about a particular method, e.g., CPM::

    rnanorm cpm --help

To normalize with CPM::

   rnanorm cpm exp.csv --out exp_cpm.csv

File ``exp.csv`` needs to be comma separated file with genes in columns and
samples in rows. Values should be raw counts. The output is saved to
``exp_cpm.csv``. Example of input file::

    cat exp.csv
    ,Gene_1,Gene_2,Gene_3,Gene_4,Gene_5
    Sample_1,200,300,500,2000,7000
    Sample_2,400,600,1000,4000,14000
    Sample_3,200,300,500,2000,17000
    Sample_4,200,300,500,2000,2000

One can also provide input through standard input::

   cat exp.csv | rnanorm cpm --out exp_cpm.csv

If file specified with ``--out`` already exists the command will fail. If you
are sure that you wish to overwrite, use ``--force`` flag::

   cat exp.csv | rnanorm cpm --force --out exp_cpm.csv

If no file is specified with ``--out`` parameter, output is printed to standard
output::

   cat exp.csv | rnanorm cpm > exp_cpm.csv

Methods TPM and FPKM require gene lengths. These can be provided either with GTF_
file or with "gene lengths" file. The later is a two columns file. The first
column should include the genes in the header of ``exp.csv`` and the second
column should contain gene lengths computed by union exon model::

    # Use GTF file
    rnanorm tpm exp.csv --gtf annotations.gtf > exp_out.csv
    # Use gene lengths file
    rnanorm tpm exp.csv --gene-lengths lenghts.csv > exp_out.csv
    # Example of gene lengths file
    cat lenghts.csv
    gene_id,gene_length
    Gene_1,200
    Gene_2,300
    Gene_3,500
    Gene_4,1000
    Gene_5,1000


.. _GTF: https://www.ensembl.org/info/website/upload/gff.html


Contribute
==========

To learn about contributing to the code base, read the  Contributing_ section.

.. _Contributing: docs/contributing.rst

Citing
======

If you are using RNAnorm in your research, please cite as suggested by "Cite this repository" section in the side panel of this page.
