scelvis 0.8.9
Single-cell RNA-seq data visualization
License: MIT license
Keywords: single-cell,visualization,bioinformatics

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SCelVis: Easy Single-Cell Visualization
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.. image:: https://img.shields.io/conda/dn/bioconda/scelvis.svg?label=Bioconda
    :target: https://bioconda.github.io/recipes/scelvis/README.html

.. image:: https://img.shields.io/pypi/pyversions/scelvis.svg
    :target: https://www.python.org

.. image:: https://img.shields.io/pypi/v/scelvis.svg
    :target: https://pypi.python.org/pypi/scelvis

.. image:: https://api.codacy.com/project/badge/Grade/9ee0ec1424c143dfad9977a649f917f7
    :target: https://www.codacy.com/app/bihealth/scelvis?utm_source=github.com&amp;utm_medium=referral&amp;utm_content=bihealth/scelvis&amp;utm_campaign=Badge_Grade

.. image:: https://api.codacy.com/project/badge/Coverage/9ee0ec1424c143dfad9977a649f917f7
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.. image:: https://readthedocs.org/projects/scelvis/badge/?version=latest
    :target: https://scelvis.readthedocs.io/en/latest/?badge=latest
    :alt: Documentation Status

.. image:: https://travis-ci.org/bihealth/scelvis.svg?branch=master
    :target: https://travis-ci.org/bihealth/scelvis

.. image:: https://zenodo.org/badge/185944510.svg
    :target: https://zenodo.org/badge/latestdoi/185944510

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Documentation
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The SCelVis documentation at `ReadTheDocs.org <https://scelvis.readthedocs.org>`_ contains comprehensive information including a `Tutorial <https://scelvis.readthedocs.io/en/latest/tutorial_analysis.html>`_.

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Movie
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.. image:: docs_manual/figures/scelvis_movie.gif
    :height: 400px
    :align: center

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Installation
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You can install with Pip and Bioconda or run directly via Docker.

.. code-block:: shell

    $ pip install scelvis
    # OR
    $ conda install scelvis
    # OR
    $ docker run ghcr.io/bihealth/scelvis:0.8.8-0 scelvis --help

Look up the latest version (instead of ``0.8.8-0`` to use at `here <ghcr.io/bihealth/scelvis>`_)

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Building Docker Image
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1. Push changes to Github (we need a [git tree-ish](https://stackoverflow.com/questions/4044368/what-does-tree-ish-mean-in-git), so a tag works as well as a feature branch).
2. Call ``GIT_TAG=tag-or-branch bash docker/build-docker.sh``.
3. Run with ``docker run ghcr.io/bihealth/scelvis:[version]-0``.
4. Push with ``docker push ghcr.io/bihealth/scelvis:[version]-0``. 


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History
=======


------
v0.8.9
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- avoid loading datasets just to get meta-data
- update dash imports

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v0.8.8
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- fixing problem with categorical data:wq

------
v0.8.7
------

- fixing problem with ports in HTTP URLs

------
v0.8.6
------

- bug fixes for cell filtering

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v0.8.5
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- allow text import with mtx files
- display only most frequent categories
- use `ad.raw` if present
- enable downsampling during conversion
- link to publication

------
v0.8.4
------

- fix bug in custom static folder route
- fix iRODS authentication defaults

------
v0.8.3
------

- allow custom markdowns for home screen
- enable gene-gene plots and change colormap for gene scatter

------
v0.8.2
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- fix iRODS authentication issues
- update docs for .h5ad input

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v0.8.1
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- fixing iframe sources (important if running behind reverse proxy with HTTPS)
- link documentation on home screen

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v0.8.0
------

- adding sphinx documentation for ReadTheDocs
- upload and convert with IFrames; increase size limit
- add box plots

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v0.7.3
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- fix cache timeout error

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v0.7.2
------

- fix ReferenceError
- updated README and tutorialmovie

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v0.7.1
------

- improved cache handling
- improved user feedback for filtering & differential expression

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v0.7.0
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- added conversion from .loom files
- cell filtering also supports downsampling
- added PBMC dataset hosted on figshare
- added demo movie

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v0.6.0
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- cell filtering
- differential expression

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v0.5.0
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- upgrades to Dash v1
- fixes to UI, upload and conversion
- avoid creation of dense matrices

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v0.4.1
------

- Fixing bug with specifying single ``.h5ad`` file as data source.
- Adding ``Dockerfile`` for building Docker images from intermediate versions.

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v0.4.0
------

- Adding support for HTTP(S) data sources.
- Embedding ``about.md`` information in Anndata file.
- Adding support for passing

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v0.3.0
------

- Adding example data set.
- Adding nice introduction to start page.
- Adding functionality for creating simple fake data set.
- Making import of ``ruamel_yaml`` more robust still.
- Adding tests.
- Adding Travis CI--based continuous integration tests.

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v0.2.1
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- Fixing SFTP support.
- Fixing import of ``ruamel_yaml``.

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v0.2.0
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- More refactorization.
- Fixing dependency on ``ruamel-yaml`` to ``ruamel.yaml``.
- Adding conversion feature.
- Adding upload feature.
- Adding support to load from SSHFS, FTP through pyfilesystem (no FTPS support).
- Adding support to load from iRODS, also works via tickets (pass ``?ticket=TICKET`` to the query parameters).

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v0.1.0
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Initial release.

- Everything is new!