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BiologicalProcessNetworks-1.0a5
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مشاهده بیشترتوضیحات
Identify significant connections between biological processes using gene interaction networks.
| ویژگی | مقدار |
|---|---|
| سیستم عامل | - |
| نام فایل | BiologicalProcessNetworks-1.0a5 |
| نام | BiologicalProcessNetworks |
| نسخه کتابخانه | 1.0a5 |
| نگهدارنده | [] |
| ایمیل نگهدارنده | [] |
| نویسنده | Christopher D. Lasher |
| ایمیل نویسنده | chris.lasher@gmail.com |
| آدرس صفحه اصلی | http://pypi.python.org/pypi/BiologicalProcessNetworks |
| آدرس اینترنتی | https://pypi.org/project/BiologicalProcessNetworks/ |
| مجوز | MIT License |
==================================
Python Biological Process Networks
==================================
Python Biological Process Networks (PyBPN) provides programs to detect
connections between biological processes (called "links") based on gene
interaction, expression, and annotation data. A collection of
significant links and the participating processes forms a biological
process network, or BPN.
PyBPN provides three related programs for finding BPNs, each with
different objectives:
bpln
Determines if processes are generally connected; an implementation of
the algorithm described by Dotan-Cohen *et al.* [1]_.
cbpn
Determines whether, under a particular comparison of conditions,
connections between processes are perturbed; an implementation of the
algorithm described by Lasher *et al.* [2]_.
mcmcbpn
Similar to ``cbpn``, but attempts to discover the smallest set of
connections which describes as much of the perturbation of interacting
genes as possible.
############
Availability
############
PyBPN releases are available from the `Python Package Index`_ (`PyPI`_)
at http://pypi.python.org/pypi/BiologicalProcessNetworks
PyBPN's source code is hosted on `GitHub`_ at
https://github.com/gotgenes/BiologicalProcessNetworks
############
Installation
############
The recommended way to install PyBPN is through the Python package
installer pip_, as it helps automagically manage dependencies, however,
this document also provides instructions for manual installation.
PyBPN has several third-party `dependencies`_, described below.
.. _dependencies:
Dependencies
============
PyBPN depends on the following Python versions and external Python
Packages (all available from `PyPI`_):
- Python **2.6** or **2.7**. Python 3 is not currently supported;
Python 2.5 and lower are unsupported. Check your Python version with
``python --version``. Obtain newer releases of Python from
http://python.org/download/
- ConflictsOptionParser_
- ConvUtils_ (v.1.1; currently v.2.0 is unsupported)
- fisher_
- NetworkX_ (v.1.0 or greater)
- SciPy_ (which depends on NumPy_)
If you are installing PyBPN via pip, you only need to ensure that you have
an appropriate version of Python installed on your system. If you are
manually installing PyBPN, you will need to obtain and install all
dependencies through your own means (e.g., via ``apt``, ``yum``, ``.dmg``
installs, or from source, following the package's instructions).
Installation by pip
===================
pip_ will download and install PyBPN, as well as any Python package
dependencies that are not yet installed on your system or which require
upgrading.
System-wide installation for users with administrative access
-------------------------------------------------------------
If you have administrative (e.g., sudo) access on your system, you may
install PyBPN system-wide with
::
sudo pip install BiologicalProcessNetworks
If you have not installed NumPy before hand, you may encounter an error
[3]_. In this case, try
::
pip install numpy
pip install BiologicalProcessNetworks
Local installation for non-privileged users
-------------------------------------------
If you do not have administrative, or do not wish to make a system-wide
installation of PyBPN, you can still install PyBPN and all its dependencies
using the user site-packages installation.
::
pip install --user BiologicalProcessNetworks
If you have not installed NumPy before hand, you may encounter an error
[3]_. In this case, try
::
pip install --user numpy
pip install --user BiologicalProcessNetworks
Manual Installation
===================
Once you have installed all dependencies_ and have obtained and unpacked
the source for PyBPN (e.g., by using ``tar``), move into the top level
directory of the unpacked source and run
::
python setup.py install
If you do not have administrative permissions for your computer, you can
install into the user-specific site-packages location with
::
python setup.py install --user
#####
Usage
#####
All programs accept the ``-h``/``--help`` option. Provide this option to
get a full usage string from the program, including all available
options. Below is a summary of the usage for each program and details of
common options.
BPLN
====
TODO
CBPLN
=====
TODO
MCMCBPN
=======
``mcmcbpn`` calculates a BPN which explains as much gene expression
perturbation an underlying gene-gene (or protein-protein) response
network as possible, using as few process-process links as possible.
``mcmcbpn`` performs `Markov chain Monte Carlo (MCMC)`_ in order to
effectively consider all possible links simultaneously and select an
optimal subset of them.
Basic Usage
-----------
The basic usage of ``mcmcbpn`` is as follows::
mcmcbpn [OPTIONS] INTERACTIONS_FILE ANNOTATIONS_FILE EXPRESSION_FILE
Each of the files is described below:
- ``INTERACTIONS_FILE``: a CSV file containing interactions. The file
should have two columns with headings "interactor1" and
"interactor2". It may have an optional column with the heading
"weight", whose values will be used as the weight or confidence
of the interaction. The file may have additional columns, which
will be ignored.
- ``ANNOTATIONS_FILE``: a file containing annotations. The annotations
file may be in one of two formats:
- GMT format: if the file ends with the extension ".gmt", it is
automatically parsed as a GMT-format file. The file is a
tab-separated (TSV) format with no headers. The first column
contains the annotation term. The second column contains a
description. All following columns contain gene IDs for genes
annotated by that term. `Full GMT format specification`_ is
available from the `MSigDB and GSEA website`_.
- Two-column format: The file should have a column titled
"gene_id" which has the gene/gene product ID, and a column
titled "term" which contains the term with which the
gene/product is annotated. The file may have additional
columns, which will be ignored.
- ``EXPRESSION_FILE``: a CSV file of gene (or gene product) expression
values. The file should have a column titled "id" which has the
gene (or gene product) ID, and a column titled "expression"
which gives a value for the expression level, or difference in
expression levels.
``mcmcbpn`` has a large number of options which can change its behavior,
either in terms of the algorithm and parameters used, or in terms of its
output. To get a full list of options, run ::
mcmcbpn --help
Below are the most important options.
Algorithm and Parameter Options
-------------------------------
These are options which affect the algorithmic behavior or starting
state of ``mcmcbpn``.
- ``--burn-in=BURN_IN``: the number of steps to take before recording
states in the Markov chain [default: ``1000000``]
- ``--steps=STEPS``: the number of steps through the Markov chain to
observe [default: ``10000000``]
- ``--activity-threshold=ACTIVITY_THRESHOLD``: set the (differential)
expression threshold at which a gene is considered active [default:
``-log10(0.05)``]
- ``--transition-ratio=TRANSITION_RATIO``: The target ratio of proposed
link transitions to proposed parameter transitions [default: ``0.9``]
- ``--fixed-distributions``: use fixed distributions for link (and term)
prior [implies ``--free-parameters]`` (**highly recommended**)
- ``--free-parameters``: parameters will be adjusted randomly, rather
than incrementally (**recommended**)
- ``--disable-swaps``: disables swapping links as an option for
transitions (**highly recommended**; will become the default option in
future releases)
Output Options
--------------
These are options which affect the output file paths and file formats
for ``mcmcbpn``.
- ``--links-outfile=LINKS_OUTFILE``: the file to which the links results
should be written [default: ``links_results.tsv``]
- ``--parameters-outfile=PARAMETERS_OUTFILE``: the file to which the
parameters results should be written [default: parameter_results.tsv]
- ``--terms-outfile=TERMS_OUTFILE``: the file to which the terms results
should be written [default: terms_results.tsv]
- ``--transitions-outfile=TRANSITIONS_OUTFILE``: the file to which the
transitions data should be written [default: transitions.tsv]
- ``--detailed-transitions``: transitions file includes full information
about each step's state (see also ``--bzip2`` below, as this can
drastically increase the file size of the transitions outfile)
- ``--bzip2``: compress transitions file using bzip2 (**highly
recommended**, the transitions file can consume a large amount of disk
space, in proportion to the number of steps)
- ``--record-frequencies``: record the frequency of each state
- ``--frequencies-outfile=FREQUENCIES_OUTFILE``: the file to which
frequency information should be written [default:
``state_frequencies.tsv``]
- ``--logfile=LOGFILE``: the file to which information for the run will
be logged [default: ``mcmcbpn-TIMESTAMP.log``]
Output
------
The two principal files output by ``mcmcbpn`` are the links outfile and
the parameters outfile.
Links File
This TSV file contains three columns: ``term1``, ``term2``, and
``probability``. ``term1`` and ``term2`` represent the two biological
processes of a given link, and ``probability`` represents the
probability that link should exist in the final biological process
network (BPN) as determined by a given run of ``mcmcbpn``.
Parameters File
This TSV file contains three columns: the first column, ``parameter``,
represents the name of the given parameter. Names include the
following:
- ``link_false_neg``: proportion of interactions not explained by the
BPN that should be
- ``link_false_pos``: propotion of interactions explained by the BPN
that should not be
- ``link_prior``: the prior probability a link would be included in
the BPN at all
The second column, ``value``, shows a particular value for a given
parameter. The third column, ``probability``, gives the estimated
probability that the given ``parameter`` should assume the respective
``value`` in order to maximize the likelihood of the BPN.
.. [1] `Dotan-Cohen, D., *et al.* "Biological Process Linkage Networks."
PLoS One. 2009. <http://dx.doi.org/10.1371/journal.pone.0005313>`_
.. [2] `Lasher, C., *et al.* "Discovering Networks of Perturbed
Biological Processes in Hepatocyte Cultures." PLoS One. 2010.
<http://dx.doi.org/10.1371/journal.pone.0015247>`_
.. [3] If your install fails during the installation of SciPy, try
running ``pip install numpy`` (or local-install equivalent) prior to
installing PyBPN.
.. _PyPI:
.. _Python Package Index: http://pypi.python.org/
.. _GitHub: https://github.com/
.. _pip: http://pypi.python.org/pypi/pip
.. _virtualenv: http://pypi.python.org/pypi/virtualenv
.. _virtualenvwrapper: http://www.doughellmann.com/projects/virtualenvwrapper/
.. _ConflictsOptionParser: http://pypi.python.org/pypi/ConflictsOptionParser/
.. _ConvUtils: http://pypi.python.org/pypi/ConvUtils/
.. _fisher: http://pypi.python.org/pypi/fisher/
.. _NetworkX: http://networkx.lanl.gov/
.. _NumPy: http://numpy.scipy.org/
.. _SciPy: http://scipy.org/
.. _`Markov chain Monte Carlo (MCMC)`: http://en.wikipedia.org/wiki/Markov_chain_Monte_Carlo
.. _`Full GMT format specification`: http://www.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats#GMT:_Gene_Matrix_Transposed_file_format_.28.2A.gmt.29
.. _MSigDB and GSEA website: http://www.broadinstitute.org/gsea/
نحوه نصب
نصب پکیج whl BiologicalProcessNetworks-1.0a5:
pip install BiologicalProcessNetworks-1.0a5.whl
نصب پکیج tar.gz BiologicalProcessNetworks-1.0a5:
pip install BiologicalProcessNetworks-1.0a5.tar.gz