semvec/pypi-packages huggingface dataset:
django-systemjs 1.4.3
Brings SystemJS to Django staticfiles
License: MIT

=====================
Django SystemJS
=====================

.. image:: https://travis-ci.org/sergei-maertens/django-systemjs.svg?branch=master
    :target: https://travis-ci.org/sergei-maertens/django-systemjs


.. image:: https://coveralls.io/repos/sergei-maertens/django-systemjs/badge.svg
  :target: https://coveralls.io/r/sergei-maertens/django-systemjs

.. image:: https://img.shields.io/pypi/v/django-systemjs.svg
  :target: https://pypi.python.org/pypi/django-systemjs


.. image:: https://readthedocs.org/projects/django-systemjs/badge/?version=latest
    :target: http://django-systemjs.readthedocs.org/en/latest/?badge=latest
    :alt: Documentation Status


Django SystemJS brings the Javascript of tomorrow to Django, today.

It leverages JSPM (https://jspm.io) to do the heavy lifting for your
client side code, while keeping development flow easy and deployment
without worries. In DEBUG mode, your Javascript modules are loaded
asynchronously. In production, your app is nicely bundled via JSPM
and ties in perfectly with `django.contrib.staticfiles`.


Installation
============

Follow the documentation on http://django-systemjs.readthedocs.org/en/latest/.
libdiatonic 0.1
Library for modeling music theory constructs
License: MIT
Keywords: music theory

libdiatonic
===========

A python 3 library for modeling music theory

|PyPI| |build status| |coverage report|

Installation
------------

``libdiatonic`` can be installed from pypi!

``pip install libdiatonic``

Usage
-----

TODO: real documentation :unamused:

For the time being, the code is littered with doctests which provide
example usage of the various classes. Please have a look around!

License
-------

This software is free to use under the
`MIT <https://opensource.org/licenses/MIT>`__ license.

.. |PyPI| image:: https://img.shields.io/pypi/v/libdiatonic.svg
   :target: https://pypi.python.org/pypi/libdiatonic
.. |build status| image:: https://gitlab.com/ajk8/libdiatonic/badges/master/build.svg
   :target: https://gitlab.com/ajk8/libdiatonic/commits/master
.. |coverage report| image:: https://gitlab.com/ajk8/libdiatonic/badges/master/coverage.svg
   :target: https://gitlab.com/ajk8/libdiatonic/commits/master
cdpipelines 0.0.7
Various bioinformatics pipelines.
License: MIT
Keywords: bioinformatics

cdpipelines
===========

This repository holds various bioinformatics pipelines.

Dependencies
------------

Many of the pipeline dependencies can be obtained using the ``prepare``
submodule (see below). Additionally, a working Python environment is
needed along with some of the common scientific python packages. I
recommend using `Anaconda
python <https://store.continuum.io/cshop/anaconda/>`__ since it includes
most of the needed packages. If you are using Anaconda, I'd recommend
making new environments for different projects. Besides the default
Anaconda packages, you will need the following (available through
``conda`` or ``pip``):

-  HTSeq
-  pandas
-  pysam (this is available through conda but currently it's an old
   version so you have to get it using ``pip``)
-  PyVCF

``rpy2``
~~~~~~~~

Installing ``rpy2`` can be tricky. Different versions of ``R`` and
``rpy2`` don't work well together, so it's recommended to make a local
installation of ``R`` using the ``prepare`` submodule and compile
``rpy2`` against this installation. You can install ``R`` using
``prepare.download_r`` and install ``rpy2`` using
``prepare.download_install_rpy2``. ``prepare.download_install_rpy2``
will prompt you to set your PATH, LDFLAGS, and LD\_LIBRARY\_PATH to
correctly install ``rpy2``. After installing ``rpy2``, you need to set
your PATH and LD\_LIBRARY\_PATH using these commands for every bash
session where you want to use this ``rpy2``. I'd recommend putting the
commands in a file that you source every time you load the project's
Anaconda environment.

Submodules
----------

``general``
~~~~~~~~~~~

``general`` contains methods used in multiple pipelines. Some pipelines
use similar but different versions of some methods, so the pipelines
will have their own versions of those methods. Sometimes it may make
sense to add options to a particular method that is used in multiple
pipelines (where each pipeline has slightly different versions) and add
the method into ``general``.

``prepare``
~~~~~~~~~~~

The ``prepare`` module contains functions for downloading various
software and reference files needed for the different pipelines.

``rnaseq``
~~~~~~~~~~

This pipeline currently starts from fastq files and has two steps. For
detailed information on each step, so the docstrings for each method.
The first step is ``align_and_sort`` which (optionally) removes
duplicates, aligns the reads, and makes coverage bigwig files for use
with the UCSC genome browser or IGV. The read alignments are output in
both genomic and transcriptomic coordinates. The second step is
``get_counts`` which counts reads overlapping genes for gene
differential expression and exonic bins for use with DEXSeq.