Python-2.7.13-foss-2016b-fh2

Package List

• APScheduler-3.3.1 In-process task scheduler with Cron-like capabilities
• Babel-2.4.0 Internationalization utilities
• BreaKmer 0.0.7
• CNVkit-0.8.5 Copy number variation toolkit for high-throughput sequencing.
• ConfigArgParse-0.11.0 A drop-in replacement for argparse that allows options to also be set via config files and/or environment variables.
• Cycler-0.10.0 Composable style cycles
• Cython-0.25.2 The Cython compiler for writing C extensions for the Python language.
• Flask-0.12.1 A simple framework for building complex web applications.
• Flask-Bootstrap-3.3.7.1 An extension that includes Bootstrap in your project, without any boilerplate code.
• Flask-Debug-0.4.3 Shows reflection/configuration to aid the development of Flask applications.
• Flask-Migrate-2.0.3 SQLAlchemy database migrations for Flask applications using Alembic
• Flask-SQLAlchemy-2.2 Adds SQLAlchemy support to your Flask application
• Flask-Script-2.0.5 Scripting support for Flask
• Flask-WTF-0.14.2 Simple integration of Flask and WTForms.
• GitPython-2.1.3 Python Git Library
• HTSeq-0.7.2 A framework to process and analyze data from high-throughput sequencing (HTS) assays
• ImmuneDB-0.19.1 A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data
• Jinja2-2.9.6 A small but fast and easy to use stand-alone template engine written in pure python.
• Keras-2.0.6 Deep Learning for humans
• MACS2-2.1.1.20160309 Model Based Analysis for ChIP-Seq data
• Mako-1.0.6 A super-fast templating language that borrows the best ideas from the existing templating languages.
• Markdown-2.6.8 Python implementation of Markdown.
• MySQL-python-1.2.5 Python interface to MySQL
• Nuitka-0.5.25 Python compiler with full language support and CPython compatibility
• PrettyTable-0.7.2 A simple Python library for easily displaying tabular data in a visually appealing ASCII table format.
• PyClone 0.12.9
• PyDP 0.2.2
• PyInstaller-3.2.1 PyInstaller bundles a Python application and all its dependencies into a single package.
• PyMySQL-0.7.11 Pure Python MySQL Driver
• PyVCF-0.6.8 Variant Call Format (VCF) parser for Python
• PyYAML-3.12 YAML parser and emitter for Python
• Pygments-2.2.0 Pygments is a syntax highlighting package written in Python.
• SQLAlchemy-1.1.9 Database Abstraction Library
• Theano-0.9.0 Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs.
• WTForms-2.1 A flexible forms validation and rendering library for Python web development.
• alnvu-0.1.0 Reformat and condense multiple sequence alignments to highlight variability
• ansible-2.3.0.0 Radically simple IT automation
• appdirs-1.4.3 A small Python module for determining appropriate platform-specific dirs, e.g. a “user data dir”.
• argparse-1.4.0 Python command-line parsing library
• astroid-1.5.2 A abstract syntax tree for Python with inference support.
• awscli-1.11.162 Universal Command Line Environment for AWS.
• backports.shutil_get_terminal_size-1.0.0 A backport of the get_terminal_size function from Python 3.3’s shutil.
• backports.weakref-1.0rc1 Backport of new features in Python’s weakref module
• bcbio-gff-0.6.4 Read and write Generic Feature Format (GFF) with Biopython integration.
• beautifulsoup4-4.5.3 Screen-scraping library
• biopython-1.69 Freely available tools for computational molecular biology.
• bitstring-3.1.5 Simple construction, analysis and modification of binary data.
• bokeh-0.12.5 Interactive plots and applications in the browser from Python
• boto3-1.4.4 The AWS SDK for Python
• brewer2mpl-1.4.1 Connect colorbrewer2.org color maps to Python and matplotlib
• certifi-2017.4.17 Python package for providing Mozilla’s CA Bundle.
• cliff-2.6.0 Command Line Interface Formulation Framework
• cmd2-0.7.0 cmd2 - a tool for building interactive command line applications in Python
• cpv-0.46 combine p-values
• cruzdb-0.5.6 Interface to UCSC genomic databases. Also allows things like up/downstream/k-nearest-neighbor queries and mirroring of tables to local sqlite databases
• cryptography-1.8.1 cryptography is a package which provides cryptographic recipes and primitives to Python developers.
• cutadapt-1.13 trim adapters from high-throughput sequencing reads
• cyvcf2-0.7.4 fast vcf parsing with cython + htslib
• darkslide-2.3.3 Lightweight markup language-based html5 slideshow generator. Forked from Landslide.
• deap-1.0.2 Distributed Evolutionary Algorithms in Python
• debtcollector-1.13.0 A collection of Python deprecation patterns and strategies that help you collect your technical debt in a non-destructive manner.
• decorator-4.0.11 Better living through Python with decorators
• deepTools-2.5.0.1 Useful tools for exploring deep sequencing data
• deprecation-1.0.1 A library to handle automated deprecations
• docutils-0.13.1 Docutils – Python Documentation Utilities
• drmaa-0.7.7 a python DRMAA library
• easygui-0.98.1 EasyGUI is a module for very simple, very easy GUI programming in Python. EasyGUI is different from other GUI generators in that EasyGUI is NOT event-driven. Instead, all GUI interactions are invoked by simple function calls.
• ecdsa-0.13 ECDSA cryptographic signature library (pure python)
• enum34-1.1.6 Python 3.4 Enum backported to 3.3, 3.2, 3.1, 2.7, 2.6, 2.5, and 2.4
• fasteners-0.14.1 A python package that provides useful locks.
• flask-appconfig-0.11.1 Configures Flask applications in a canonical way. Also auto-configures Heroku. Aims to standardize configuration.
• flask-nav-0.6 Easily create navigation for Flask applications.
• freezer-5.0.0.0b1 The OpenStack Backup Restore and Disaster Recovery as a Service Platform
• funcsigs-1.0.2 Python function signatures from PEP362 for Python 2.6, 2.7 and 3.2+
• functools32-3.2.3-2 Backport of the functools module from Python 3.2.3 for use on 2.7 and PyPy.
• futures-3.1.1 Backport of the concurrent.futures package from Python 3
• geneimpacts-0.3.2 normalize effects from variant annotation tools (snpEff, VEP)
• gitdb2-2.0.0 Git Object Database
• google-1.9.3 Python bindings to the Google search engine.
• h5py-2.7.0 Read and write HDF5 files from Python
• html5lib-0.999999999 HTML parser based on the WHATWG HTML specification
• ipython_genutils-0.2.0 Vestigial utilities from IPython
• iso8601-0.1.11 Simple module to parse ISO 8601 dates
• jellyfish-0.5.6 a library for doing approximate and phonetic matching of strings.
• keystoneauth1-2.20.0 Authentication Library for OpenStack Identity
• ldap3-2.2.3 A strictly RFC 4510 conforming LDAP V3 pure Python client library
• liac-arff-2.1.0 A module for read and write ARFF files in Python.
• lockfile-0.12.2 Platform-independent file locking module
• lxml-3.7.3 Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API.
• matplotlib-2.0.1 Python plotting package
• messytables-0.15.2 Parse messy tabular data in various formats
• mincemeat-0.1.4 UNKNOWN
• misopy-0.5.3 Mixture of Isoforms model (MISO) for isoform quantitation using RNA-Seq
• mock-2.0.0 Rolling backport of unittest.mock for all Pythons
• monotonic-1.3 An implementation of time.monotonic() for Python 2 & < 3.3
• mpi4py-2.0.0 Python bindings for MPI
• msgpack-python-0.4.8 MessagePack (de)serializer.
• ndg-httpsclient-0.4.2 Provides enhanced HTTPS support for httplib and urllib2 using PyOpenSSL
• netCDF4-1.2.7 Provides an object-oriented python interface to the netCDF version 4 library.
• netaddr-0.7.19 A network address manipulation library for Python
• netifaces-0.10.5 Portable network interface information.
• networkx-1.11 Python package for creating and manipulating graphs and networks
• nose-1.3.7 nose extends unittest to make testing easier
• np_utils-0.5.3.3 collection of utilities for array and list manipulation
• npyscreen-4.10.5 Writing user interfaces without all that ugly mucking about in hyperspace
• numpy-1.12.1 NumPy: array processing for numbers, strings, records, and objects.
• oauth-1.0.1 Library for OAuth version 1.0a.
• opencv_python-3.3.0.10 Wrapper package for OpenCV python bindings.
• openstacksdk-0.9.16 An SDK for building applications to work with OpenStack
• os-client-config-1.27.0 OpenStack Client Configuation Library
• osc-lib-1.6.0 OpenStackClient Library
• oslo.concurrency-3.20.0 Oslo Concurrency library
• oslo.config-4.1.0 Oslo Configuration API
• oslo.context-2.13.0 Oslo Context library
• oslo.i18n-3.15.0 Oslo i18n library
• oslo.log-3.26.0 oslo.log library
• oslo.serialization-2.18.0 Oslo Serialization library
• oslo.utils-3.25.0 Oslo Utility library
• packaging-16.8 Core utilities for Python packages
• pandas-0.20.0rc1 Powerful data structures for data analysis, time series, and statistics
• paramiko-2.1.2 SSH2 protocol library
• pathlib2-2.2.1 Object-oriented filesystem paths
• paycheck-1.0.2 A Python QuickCheck implementation
• pbr-3.0.0 Python Build Reasonableness
• peddy-0.2.9 pleasingly pythonic pedigree manipulation
• pep8-1.7.0 Python style guide checker
• pickleshare-0.7.4 Tiny ‘shelve’-like database with concurrency support
• pip-9.0.1 The PyPA recommended tool for installing Python packages.
• poretools-0.6.0 A toolset for working with nanopore sequencing data
• positional-1.1.1 Library to enforce positional or key-word arguments (deprecated/unmaintained)
• prompt_toolkit-1.0.14 Library for building powerful interactive command lines in Python
• protobuf-3.3.0 Protocol Buffers
• psutil-5.2.2 Cross-platform lib for process and system monitoring in Python.
• psycopg2-2.7.1 psycopg2 - Python-PostgreSQL Database Adapter
• pyBigWig-0.3.4 A package for accessing bigWig files using libBigWig
• pyOpenSSL-17.0.0 Python wrapper module around the OpenSSL library
• pyasn1-0.2.3 ASN.1 types and codecs
• pyastro-1.1 Astronomical Library
• pycrypto-2.6.1 Cryptographic modules for Python.
• pycurl-7.43.0 PycURL – A Python Interface To The cURL library
• pydicom-0.9.9 Pure python package for DICOM medical file reading and writing
• pyensembl-1.1.0 Python interface to ensembl reference genome metadata
• pygithub3-0.5.1 Python wrapper for the github v3 api
• pyinotify-0.9.6 Linux filesystem events monitoring
• pymongo-3.4.0 Python driver for MongoDB http://www.mongodb.org
• pymssql-2.1.3 DB-API interface to Microsoft SQL Server for Python. (new Cython-based version)
• pypandoc-1.4 Thin wrapper for pandoc.
• pyparsing-2.2.0 Python parsing module
• pysam-0.11.1 pysam
• python-cinderclient-2.0.1 OpenStack Block Storage API Client Library
• python-dateutil-2.6.0 Extensions to the standard Python datetime module
• python-freezerclient-1.4.0 OpenStack Disaster Recovery API Client Library
• python-glanceclient-2.6.0 OpenStack Image API Client Library
• python-keystoneclient-3.10.0 Client Library for OpenStack Identity
• python-memcached-1.58 Pure python memcached client
• python-novaclient-8.0.0 Client library for OpenStack Compute API
• python-openstackclient-3.10.0 OpenStack Command-line Client
• python-pam-1.8.2 Python PAM module using ctypes, py3/py2
• python-snappy-0.5 Python library for the snappy compression library from Google
• python-swiftclient-3.3.0 OpenStack Object Storage API Client Library
• pytz-2017.2 World timezone definitions, modern and historical
• qiime-1.9.1 Quantitative Insights Into Microbial Ecology
• qrcode-5.3 QR Code image generator
• requests-2.13.0 Python HTTP for Humans.
• requestsexceptions-1.2.0 Import exceptions from potentially bundled packages in requests.
• rfc3986-0.4.1 Validating URI References per RFC 3986
• scikit-learn-0.18.1 A set of python modules for machine learning and data mining
• scipy-0.19.0 SciPy: Scientific Library for Python
• seaborn-0.7.1 Seaborn: statistical data visualization
• seqmagick-0.6.1 Tools for converting and modifying sequence files from the command-line
• setuptools-35.0.2 Easily download, build, install, upgrade, and uninstall Python packages
• shove-0.6.6 Generic dictionaryish object storage frontend
• simplegeneric-0.8.1 Simple generic functions (similar to Python’s own len(), pickle.dump(), etc.)
• simplejson-3.10.0 Simple, fast, extensible JSON encoder/decoder for Python
• six-1.10.0 Python 2 and 3 compatibility utilities
• slurm-pipeline-1.1.1 A Python class for scheduling SLURM jobs
• smmap2-2.0.1 A pure python implementation of a sliding window memory map manager
• stevedore-1.21.0 Manage dynamic plugins for Python applications
• tensorflow-1.3.0rc2 TensorFlow helps the tensors flow
• toil-3.8.0a1.dev393 Pipeline management software for clusters.
• toolshed-0.4.6 Tools for data
• traitlets-4.3.2 Traitlets Python config system
• twobitreader-3.1.4 A fast python package for reading .2bit files (used by the UCSC genome browser)
• tzlocal-1.4 tzinfo object for the local timezone
• umi_tools-0.5.0 umi_tools: Tools for UMI analyses
• umis-0.7.0 Package for estimating UMI counts in Transcript Tag Counting data.
• unicodecsv-0.14.1 Python2’s stdlib csv module is nice, but it doesn’t support unicode. This module is a drop-in replacement which does.
• uritemplate-3.0.0 URI templates
• urwid-1.3.1 A full-featured console (xterm et al.) user interface library
• vctools-0.1.6.1 A set of tools for interacting with the VMware vCloud API, whether on vCloud Air or locally installed.
• virtualenv-15.1.0 Virtual Python Environment builder
• warlock-1.3.0 Python object model built on JSON schema and JSON patch.
• watchdog-0.8.3 Filesystem events monitoring
• wrapt-1.10.10 Module for decorators, wrappers and monkey patching.