fhPython-3.9.6-foss-2021b

Package List

• APScheduler-3.9.1 In-process task scheduler with Cron-like capabilities
• Automat-20.2.0 Self-service finite-state machines for the programmer on the go.
• Babel-2.10.3 Internationalization utilities
• Biopython 1.79 Module
• Bottleneck-1.3.2 Fast NumPy array functions written in C
• Brotli-1.0.9 Python bindings for the Brotli compression library
• CacheControl-0.12.11 httplib2 caching for requests
• CellBender 0.2.1
• ConfigArgParse-1.5.3 A drop-in replacement for argparse that allows options to also be set via config files and/or environment variables.
• Cycler-0.11.0 Composable style cycles
• Cython-0.29.24 The Cython compiler for writing C extensions for the Python language.
• DCA-0.3.4 Count autoencoder for scRNA-seq denoising
• DataShape-0.5.2 A data description language.
• DateTime-4.5 This package provides a DateTime data type, as known from Zope. Unless you need to communicate with Zope APIs, you’re probably better off using Python’s built-in datetime module.
• DendroPy-4.5.2 A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters.
• Deprecated-1.2.13 Python @deprecated decorator to deprecate old python classes, functions or methods.
• Django-4.0.6 A high-level Python web framework that encourages rapid development and clean, pragmatic design.
• Flask-2.1.2 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-Cors-3.0.10 A Flask extension adding a decorator for CORS support
• Flask-Debug-0.4.3 Shows reflection/configuration to aid the development of Flask applications.
• Flask-Migrate-3.1.0 SQLAlchemy database migrations for Flask applications using Alembic.
• Flask-SQLAlchemy-2.5.1 Adds SQLAlchemy support to your Flask application.
• Flask-WTF-1.0.1 Form rendering, validation, and CSRF protection for Flask with WTForms.
• Genshi-0.7.7 A toolkit for generation of output for the web
• GitPython-3.1.27 GitPython is a python library used to interact with Git repositories
• HTSeq-2.0.2 A framework to process and analyze data from high-throughput sequencing (HTS) assays
• HeapDict-1.0.1 a heap with decrease-key and increase-key operations
• IPython 7.26.0 Module
• Jinja2-3.1.2 A very fast and expressive template engine.
• Logbook-1.5.3 A logging replacement for Python
• Mako-1.2.1 A super-fast templating language that borrows the best ideas from the existing templating languages.
• Markdown-3.3.7 Python implementation of Markdown.
• MarkupSafe-2.1.1 Safely add untrusted strings to HTML/XML markup.
• MonkeyType-22.2.0 Generating type annotations from sampled production types
• Morfessor-2.0.6 Morfessor
• NanoComp-1.19.0 Comparing runs of Oxford Nanopore sequencing data and alignments
• NanoFilt-2.8.0 Filtering and trimming of Oxford Nanopore Sequencing data
• NanoLyse-1.2.0 Removing reads mapping to the lambda genome
• NanoPlot-1.40.0 Plotting suite for Oxford Nanopore sequencing data and alignments
• NanoStat-1.6.0 Calculate statistics for Oxford Nanopore sequencing data and alignments
• Nuitka-0.9.4 Python compiler with full language support and CPython compatibility
• POT-0.8.2 Python Optimal Transport Library
• Parsley-1.3 Parsing and pattern matching made easy.
• Paste-3.5.1 Tools for using a Web Server Gateway Interface stack
• PasteDeploy-2.1.1 Load, configure, and compose WSGI applications and servers
• Pillow 8.3.2 Module
• Porechop 0.2.4 Module
• PuLP-2.6.0 PuLP is an LP modeler written in python. PuLP can generate MPS or LP files and call GLPK, COIN CLP/CBC, CPLEX, and GUROBI to solve linear problems.
• PyChef-0.3.0 Python implementation of a Chef API client.
• PyDP-0.2.4 Data Processing Lib
• PyGithub-1.55 Use the full Github API v3
• PyGreSQL-5.2.4 Python PostgreSQL Interfaces
• PyJWT-2.4.0 JSON Web Token implementation in Python
• PyMySQL-1.0.2 Pure Python MySQL Driver
• PyNaCl-1.5.0 Python binding to the Networking and Cryptography (NaCl) library
• PyOpenGL-3.1.6 Standard OpenGL bindings for Python
• PyTables 3.6.1 Module
• PyVCF-0.6.8 Variant Call Format (VCF) parser for Python
• PyWavelets-1.2.0 PyWavelets, wavelet transform module
• PyYAML 5.4.1 Module
• Pygments-2.12.0 Pygments is a syntax highlighting package written in Python.
• Pyro4-4.82 distributed object middleware for Python (RPC)
• Pysam 0.18.0 Module
• Routes-2.5.1 Routing Recognition and Generation Tools
• SPARQLWrapper-2.0.0 SPARQL Endpoint interface to Python
• SQLAlchemy-1.4.39 Database Abstraction Library
• SciPy-bundle 2021.10 Module
• SecretStorage-3.3.1 Python bindings to FreeDesktop.org Secret Service API
• Send2Trash-1.8.0 Send file to trash natively under Mac OS X, Windows and Linux.
• Sphinx-5.0.2 Python documentation generator
• Tempita-0.5.2 A very small text templating language
• Theano-1.0.5 Optimizing compiler for evaluating mathematical expressions on CPUs and GPUs.
• Twisted-22.4.0 An asynchronous networking framework written in Python
• WTForms-3.0.1 Form validation and rendering for Python web development.
• WebOb-1.8.7 WSGI request and response object
• Werkzeug-2.1.2 The comprehensive WSGI web application library.
• XlsxWriter-3.0.3 A Python module for creating Excel XLSX files.
• ZConfig-3.6.0 Structured Configuration Library
• absl-py-1.1.0 Abseil Python Common Libraries, see https://github.com/abseil/abseil-py.
• abstract_rendering-0.5.1 Rendering as a binning process
• adal-1.2.7 Note: This library is already replaced by MSAL Python, available here: https://pypi.org/project/msal/ .ADAL Python remains available here as a legacy. The ADAL for Python library makes it easy for python application to authenticate to Azure Active Directory (AAD) in order to access AAD protected web resources.
• aenum-3.1.11 Advanced Enumerations (compatible with Python’s stdlib Enum), NamedTuples, and NamedConstants
• aiobotocore-2.3.4 Async client for aws services using botocore and aiohttp
• aiodns-3.0.0 Simple DNS resolver for asyncio
• aiohttp-3.8.1 Async http client/server framework (asyncio)
• aioitertools-0.10.0 itertools and builtins for AsyncIO and mixed iterables
• aiosignal-1.2.0 aiosignal: a list of registered asynchronous callbacks
• airr-1.3.1 AIRR Community Data Representation Standard reference library for antibody and TCR sequencing data.
• alabaster-0.7.12 A configurable sidebar-enabled Sphinx theme
• alembic-1.8.1 A database migration tool for SQLAlchemy.
• alnvu-0.3.3 Reformat and condense multiple sequence alignments to highlight variability
• altair-4.2.0 Altair: A declarative statistical visualization library for Python.
• altgraph-0.17.2 Python graph (network) package
• amqp-5.1.1 Low-level AMQP client for Python (fork of amqplib).
• anndata-0.8.0 Annotated data.
• annoy-1.17.0 Approximate Nearest Neighbors in C++/Python optimized for memory usage and loading/saving to disk.
• ansible-6.1.0 Radically simple IT automation
• ansible-core-2.13.1 Radically simple IT automation
• anyio-3.6.1 High level compatibility layer for multiple asynchronous event loop implementations
• apipkg-3.0.1 apipkg: namespace control and lazy-import mechanism
• apiwrapper-0.1.8 Simple API Wrapper
• appdirs-1.4.4 A small Python module for determining appropriate platform-specific dirs, e.g. a “user data dir”.
• appnope-0.1.3 Disable App Nap on macOS >= 10.9
• argcomplete-2.0.0 Bash tab completion for argparse
• argh-0.26.2 An unobtrusive argparse wrapper with natural syntax
• argon2-cffi-20.1.0 The secure Argon2 password hashing algorithm.
• argon2-cffi-bindings-21.2.0 Low-level CFFI bindings for Argon2
• arrow-1.2.2 Better dates & times for Python
• asciitree-0.3.3 Draws ASCII trees.
• asgiref-3.5.2 ASGI specs, helper code, and adapters
• asn1crypto-1.4.0 Fast ASN.1 parser and serializer with definitions for private keys, public keys, certificates, CRL, OCSP, CMS, PKCS#3, PKCS#7, PKCS#8, PKCS#12, PKCS#5, X.509 and TSP
• astor-0.8.1 Read/rewrite/write Python ASTs
• asttokens-2.0.5 Annotate AST trees with source code positions
• astunparse-1.6.3 An AST unparser for Python
• async-timeout-4.0.2 Timeout context manager for asyncio programs
• async_generator-1.10 Async generators and context managers for Python 3.5+
• asynctest-0.13.0 Enhance the standard unittest package with features for testing asyncio libraries
• atomicwrites-1.4.0 Atomic file writes.
• attrs-21.4.0 Classes Without Boilerplate
• autograd-1.4 Efficiently computes derivatives of numpy code.
• autograd_gamma-0.5.0 Autograd compatible approximations to the gamma family of functions
• autopage-0.5.1 A library to provide automatic paging for console output
• autopep8-1.6.0 A tool that automatically formats Python code to conform to the PEP 8 style guide
• azure-core-1.24.2 Microsoft Azure Core Library for Python
• backcall-0.2.0 Specifications for callback functions passed in to an API
• backports.cached-property-1.0.2 cached_property() - computed once per instance, cached as attribute
• backports.entry_points_selectable-1.1.0 Compatibility shim providing selectable entry points for older implementations
• backports.functools-lru-cache-1.6.4 Backport of functools.lru_cache
• backports.functools_lru_cache-1.6.4 Backport of functools.lru_cache
• backports.shutil_get_terminal_size-1.0.0 A backport of the get_terminal_size function from Python 3.3’s shutil.
• backports.weakref-1.0.post1 Backport of new features in Python’s weakref module
• backports.zoneinfo-0.2.1 Backport of the standard library zoneinfo module
• bagit-1.8.1 Create and validate BagIt packages
• bandit-1.7.4 Security oriented static analyser for python code.
• bbknn-1.5.1 Batch balanced KNN
• bcbio-gff-0.6.9 Read and write Generic Feature Format (GFF) with Biopython integration.
• bcrypt-3.2.0 Modern password hashing for your software and your servers
• bd2k-python-lib-1.14a1.dev48 The BD2K Python module kitchen sink
• beautifulsoup4-4.11.1 Screen-scraping library
• beniget-0.4.1 Extract semantic information about static Python code
• betamax-0.8.1 A VCR imitation for python-requests
• billiard-4.0.0 Python multiprocessing fork with improvements and bugfixes
• biolib-0.1.9 Package for common tasks in bioinformatics.
• bitarray-2.5.1 efficient arrays of booleans – C extension
• bitstring-3.1.9 Simple construction, analysis and modification of binary data.
• black-22.6.0 The uncompromising code formatter.
• bleach-4.0.0 An easy safelist-based HTML-sanitizing tool.
• blessings-1.7 A thin, practical wrapper around terminal coloring, styling, and positioning
• blinker-1.4 Fast, simple object-to-object and broadcast signaling
• blist-1.3.6 a list-like type with better asymptotic performance and similar performance on small lists
• bokeh-2.4.3 Interactive plots and applications in the browser from Python
• boltons-21.0.0 When they’re not builtins, they’re boltons.
• boto3-1.24.28 The AWS SDK for Python
• botocore-1.27.28 Low-level, data-driven core of boto 3.
• bpython-0.22.1
• brotlipy-0.7.0 Python binding to the Brotli library
• burrito-0.9.1 Framework for wrapping and controlling command-line applications.
• burrito-fillings-0.1.1 burrito-fillings: burrito application controllers for bioinformatics
• bz2file-0.98 Read and write bzip2-compressed files.
• cached-property-1.5.2 A decorator for caching properties in classes.
• cachy-0.3.0 Cachy provides a simple yet effective caching library.
• capturer-3.0 Easily capture stdout/stderr of the current process and subprocesses
• cassandra-driver-3.25.0 DataStax Driver for Apache Cassandra
• celery-5.2.7 Distributed Task Queue.
• certifi-2021.5.30 Python package for providing Mozilla’s CA Bundle.
• cffi-1.14.6 Foreign Function Interface for Python calling C code.
• cftime-1.6.1 Time-handling functionality from netcdf4-python
• changeo-1.2.0 A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
• chardet-4.0.0 Universal encoding detector for Python 3
• charset-normalizer-2.0.4 The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet.
• charset_normalizer-2.0.6 The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet.
• circlator-1.5.5 circlator: a tool to circularise genome assemblies
• cleo-0.8.1 Cleo allows you to create beautiful and testable command-line interfaces.
• click-8.1.3 Composable command line interface toolkit
• click-didyoumean-0.3.0 Enables git-like did-you-mean feature in click
• click-plugins-1.1.1 An extension module for click to enable registering CLI commands via setuptools entry-points.
• click-repl-0.2.0 REPL plugin for Click
• cliff-3.10.1 Command Line Interface Formulation Framework
• clikit-0.6.2 CliKit is a group of utilities to build beautiful and testable command line interfaces.
• cloudpickle-2.1.0 Extended pickling support for Python objects
• clyent-1.2.1 Command line client Library for windwos and posix
• cmarkgfm-0.8.0 Minimal bindings to GitHub’s fork of cmark
• cmd2-2.4.2 cmd2 - quickly build feature-rich and user-friendly interactive command line applications in Python
• codecov-2.1.12 Hosted coverage reports for GitHub, Bitbucket and Gitlab
• collective.checkdocs-0.2 Distutils command to view and validate restructured text in package’s long_description
• colorama-0.4.4 Cross-platform colored terminal text.
• coloredlogs-15.0.1 Colored terminal output for Python’s logging module
• commonmark-0.9.1 Python parser for the CommonMark Markdown spec
• configobj-5.0.6 Config file reading, writing and validation.
• configparser-5.2.0 Updated configparser from stdlib for earlier Pythons.
• connection_pool-0.0.3 thread safe connection pool
• constantly-15.1.0 Symbolic constants in Python
• contextlib2-21.6.0 Backports and enhancements for the contextlib module
• contextvars-2.4 PEP 567 Backport
• coverage-6.4.2 Code coverage measurement for Python
• coveralls-3.3.1 Show coverage stats online via coveralls.io
• crashtest-0.3.1 Manage Python errors with ease
• cryptography-3.4.7 cryptography is a package which provides cryptographic recipes and primitives to Python developers.
• cssselect-1.1.0 cssselect parses CSS3 Selectors and translates them to XPath 1.0
• curtsies-0.3.10 Curses-like terminal wrapper, with colored strings!
• cutadapt-4.1 Adapter trimming and other preprocessing of high-throughput sequencing reads
• cwcwidth-0.1.6 Python bindings for wc(s)width
• cwl-0.0.1 Common Workflow Language Command Line Interface
• cwlref-runner-1.0 Common workflow language reference implementation
• cwltool-3.1.20220628170238 Common workflow language reference implementation
• cx_Freeze-6.7 Create standalone executables from Python scripts
• cx_Logging-3.0 Python and C interfaces for logging
• cytoolz-0.12.0 Cython implementation of Toolz: High performance functional utilities
• daemonize-2.5.0 Library to enable your code run as a daemon process on Unix-like systems.
• daiquiri-3.2.1 Library to configure Python logging easily
• darkslide-6.0.0 Lightweight markup language-based html5 slideshow generator. Forked from Landslide.
• dask-2022.1.0 Parallel PyData with Task Scheduling
• dask-jobqueue-0.7.3 Deploy Dask on job queuing systems like PBS, Slurm, SGE or LSF
• dask-mpi-2021.11.0 Deploy Dask using mpi4py
• datacache-1.1.5 Helpers for transparently downloading datasets
• datrie-0.8.2 Super-fast, efficiently stored Trie for Python.
• dbf-0.99.2 Pure python package for reading/writing dBase, FoxPro, and Visual FoxPro .dbf files (including memos)
• ddt-1.5.0 Data-Driven/Decorated Tests
• deap-1.3.1 Distributed Evolutionary Algorithms in Python
• debtcollector-2.5.0 A collection of Python deprecation patterns and strategies that help you collect your technical debt in a non-destructive manner.
• debugpy-1.4.1 An implementation of the Debug Adapter Protocol for Python
• decorator-5.0.9 Decorators for Humans
• deepTools-3.5.1 Useful tools for exploring deep sequencing data
• defusedxml-0.7.1 XML bomb protection for Python stdlib modules
• dep_check-2.0.1 Python Dependency Check Tool
• deprecation-2.1.0 A library to handle automated deprecations
• dill-0.3.5.1 serialize all of python
• distlib-0.3.2 Distribution utilities
• distributed-2022.1.0 Distributed scheduler for Dask
• distro-1.7.0 Distro - an OS platform information API
• django-configurations-2.3.2 A helper for organizing Django settings.
• dnaio-0.9.0 Read and write FASTA and FASTQ files efficiently
• dnspython-2.2.1 DNS toolkit
• doc8-0.11.2 Style checker for Sphinx (or other) RST documentation
• docopt-0.6.2 Pythonic argument parser, that will make you smile
• docrep-0.3.2 Python package for docstring repetition
• docutils-0.17.1 Docutils – Python Documentation Utilities
• docutils-stubs-0.0.22 PEP 561 type stubs for docutils
• dogpile.cache-1.1.8 A caching front-end based on the Dogpile lock.
• dominate-2.6.0 Dominate is a Python library for creating and manipulating HTML documents using an elegant DOM API.
• dpath-2.0.6 Filesystem-like pathing and searching for dictionaries
• dpcontracts-0.6.0 A simple implementation of contracts for Python.
• dulwich-0.20.44 Python Git Library
• dunamai-1.12.0 Dynamic version generation
• dxpy-0.326.1 DNAnexus Platform API bindings for Python
• ecdsa-0.17.0 ECDSA cryptographic signature library (pure python)
• editables-0.3 Editable installations
• elementpath-2.5.3 XPath 1.0/2.0/3.0 parsers and selectors for ElementTree and lxml
• entrypoints-0.3 Discover and load entry points from installed packages.
• ephem-4.1.3 Compute positions of the planets and stars
• epydoc-3.0.1 Edward Loper’s API Documentation Generation Tool
• et_xmlfile-1.1.0 An implementation of lxml.xmlfile for the standard library
• eventlet-0.33.1 Highly concurrent networking library
• execnet-1.9.0 execnet: rapid multi-Python deployment
• executing-0.8.3 Get the currently executing AST node of a frame, and other information
• extras-1.0.0 Useful extra bits for Python - things that shold be in the standard library
• fastcache-1.1.0 C implementation of Python 3 functools.lru_cache
• fasteners-0.17.3 A python package that provides useful locks
• fastjsonschema-2.15.3 Fastest Python implementation of JSON schema
• fastnumbers-3.2.1 Super-fast and clean conversions to numbers.
• feather-format-0.4.1 Simple wrapper library to the Apache Arrow-based Feather File Format
• fields-5.0.0 Container class boilerplate killer.
• filelock-3.0.12 A platform independent file lock.
• findspark-2.0.1 Find pyspark to make it importable.
• first-2.0.2 Return the first true value of an iterable.
• fixtures-4.0.1 Fixtures, reusable state for writing clean tests and more.
• flake8-4.0.1 the modular source code checker: pep8 pyflakes and co
• flake8-docstrings-1.6.0 Extension for flake8 which uses pydocstyle to check docstrings
• flake8-import-order-0.18.1 Flake8 and pylama plugin that checks the ordering of import statements.
• flake8-polyfill-1.0.2 Polyfill package for Flake8 plugins
• flaky-3.7.0 Plugin for nose or pytest that automatically reruns flaky tests.
• 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.
• flatbuffers-2.0 The FlatBuffers serialization format for Python
• flit-3.3.0 A simple packaging tool for simple packages.
• flit-core-3.3.0 Distribution-building parts of Flit. See flit package for more information
• flup-1.0.3 Random assortment of WSGI servers (py3)
• formulaic-0.3.4 An implementation of Wilkinson formulas.
• freezer-12.0.0 The OpenStack Backup Restore and Disaster Recovery as a Service Platform
• frozenlist-1.3.0 A list-like structure which implements collections.abc.MutableSequence
• fsspec-2021.7.0 File-system specification
• funcsigs-1.0.2 Python function signatures from PEP362 for Python 2.6, 2.7 and 3.2+
• future-0.18.2 Clean single-source support for Python 3 and 2
• galaxy-lib-19.5.2 Subset of Galaxy (http://galaxyproject.org/) core code base designed to be used a library.
• gast-0.5.3 Python AST that abstracts the underlying Python version
• geomet-0.3.0 GeoJSON <-> WKT/WKB conversion utilities
• get_version-3.5.4 A version helper in the spirit of versioneer.
• gevent-21.12.0 Coroutine-based network library
• gitdb-4.0.9 Git Object Database
• gitdb2-4.0.2 A mirror package for gitdb
• glob2-0.7 Version of the glob module that can capture patterns and supports recursive wildcards
• gnureadline-8.1.2 The standard Python readline extension statically linked against the GNU readline library.
• google-3.0.0 Python bindings to the Google search engine.
• google-pasta-0.2.0 pasta is an AST-based Python refactoring library
• graphviz-0.20 Simple Python interface for Graphviz
• greenlet-1.1.2 Lightweight in-process concurrent programming
• grpcio-1.47.0 HTTP/2-based RPC framework
• gtfparse-1.2.1 GTF Parsing
• h11-0.13.0 A pure-Python, bring-your-own-I/O implementation of HTTP/1.1
• h2-4.0.0 HTTP/2 State-Machine based protocol implementation
• h5py-3.7.0 Read and write HDF5 files from Python
• hacking-4.1.0 OpenStack Hacking Guideline Enforcement
• hatch-1.4.2 Modern, extensible Python project management
• hatch-vcs-0.2.0 Hatch plugin for versioning with your preferred VCS
• hatchling-1.6.0 Modern, extensible Python build backend
• hdmedians-0.14.2 High-dimensional medians
• hiredis-2.0.0 Python wrapper for hiredis
• hpack-4.0.0 Pure-Python HPACK header compression
• html5lib-1.1 HTML parser based on the WHATWG HTML specification
• httpcore-0.13.7 A minimal low-level HTTP client.
• httpie-3.2.1 HTTPie: modern, user-friendly command-line HTTP client for the API era.
• httplib2-0.20.4 A comprehensive HTTP client library.
• humanfriendly-10.0 Human friendly output for text interfaces using Python
• hunter-3.4.3 Hunter is a flexible code tracing toolkit.
• hyperframe-6.0.1 HTTP/2 framing layer for Python
• hyperlink-21.0.0 A featureful, immutable, and correct URL for Python.
• hyperopt-0.2.7 Distributed Asynchronous Hyperparameter Optimization
• idna-3.2 Internationalized Domain Names in Applications (IDNA)
• idna-ssl-1.1.0 Patch ssl.match_hostname for Unicode(idna) domains support
• igraph-0.9.8 High performance graph data structures and algorithms
• ijson-3.1.4 Iterative JSON parser with standard Python iterator interfaces
• imageio-2.19.3 Library for reading and writing a wide range of image, video, scientific, and volumetric data formats.
• imagesize-1.2.0 Getting image size from png/jpeg/jpeg2000/gif file
• importlib-1.0.4 Backport of importlib.import_module() from Python 2.7
• importlib-metadata-4.12.0 Read metadata from Python packages
• importlib-resources-5.8.0 Read resources from Python packages
• importlib_metadata-4.6.3 Read metadata from Python packages
• importlib_resources-5.2.2 Read resources from Python packages
• imread-0.7.4 imread: Image reading library
• incremental-21.3.0 A small library that versions your Python projects.
• inflection-0.5.1 A port of Ruby on Rails inflector to Python
• iniconfig-1.1.1 iniconfig: brain-dead simple config-ini parsing
• interface_meta-1.3.0 interface_meta provides a convenient way to expose an extensible API with enforced method signatures and consistent documentation.
• interop-1.1.23 The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files produced by Illumina sequencers. These libraries are backwards compatible and capable of supporting prior releases of the software, with one exception: GA systems have been excluded.
• intervaltree-3.1.0 Editable interval tree data structure for Python 2 and 3
• intreehooks-1.0 Load a PEP 517 backend from inside the source tree
• ip_associations_python_novaclient_ext-0.2 Adds Rackspace ip_associations support to python-novaclient
• ipaddress-1.0.23 IPv4/IPv6 manipulation library
• ipdb-0.13.9 IPython-enabled pdb
• ipykernel-6.0.3 IPython Kernel for Jupyter
• ipython-7.26.0 IPython: Productive Interactive Computing
• ipython_genutils-0.2.0 Vestigial utilities from IPython
• ipywidgets-7.6.3 Jupyter interactive widgets
• isal-1.0.1 Faster zlib and gzip compatible compression and decompression by providing python bindings for the ISA-L library.
• iso8601-1.0.2 Simple module to parse ISO 8601 dates
• isodate-0.6.1 An ISO 8601 date/time/duration parser and formatter
• isort-5.10.1 A Python utility / library to sort Python imports.
• itsdangerous-2.1.2 Safely pass data to untrusted environments and back.
• jaraco.functools-3.5.0 Functools like those found in stdlib
• jdcal-1.4.1 Julian dates from proleptic Gregorian and Julian calendars.
• jedi-0.18.0 An autocompletion tool for Python that can be used for text editors.
• jeepney-0.7.1 Low-level, pure Python DBus protocol wrapper.
• jellyfish-0.9.0 a library for doing approximate and phonetic matching of strings.
• jmespath-1.0.1 JSON Matching Expressions
• joblib-1.0.1 Lightweight pipelining with Python functions
• json2html-1.3.0 JSON to HTML Table Representation
• json5-0.9.8 A Python implementation of the JSON5 data format.
• jsonlines-3.1.0 Library with helpers for the jsonlines file format
• jsonpatch-1.32 Apply JSON-Patches (RFC 6902)
• jsonpointer-2.3 Identify specific nodes in a JSON document (RFC 6901)
• jsonschema-3.2.0 An implementation of JSON Schema validation for Python
• jsontableschema-0.10.1 A utility library for working with JSON Table Schema in Python
• jupyter_client-6.1.12 Jupyter protocol implementation and client libraries
• jupyter_core-4.7.1 Jupyter core package. A base package on which Jupyter projects rely.
• jupyter_packaging-0.10.4 Jupyter Packaging Utilities.
• jupyterlab_pygments-0.1.2 Pygments theme using JupyterLab CSS variables
• jupyterlab_widgets-1.0.0 Jupyter interactive widgets for JupyterLab
• keepalive-0.5 urllib keepalive support for python
• keyring-23.6.0 Store and access your passwords safely.
• keyrings.alt-4.1.0 Alternate keyring implementations
• keystoneauth1-4.6.0 Authentication Library for OpenStack Identity
• kiwisolver-1.3.2 A fast implementation of the Cassowary constraint solver
• kombu-5.2.4 Messaging library for Python.
• lark-parser-0.12.0 a modern parsing library
• lazr.uri-1.0.6 A self-contained, easily reusable library for parsing, manipulating,
• lazy-object-proxy-1.7.1 A fast and thorough lazy object proxy.
• ldap3-2.9.1 A strictly RFC 4510 conforming LDAP V3 pure Python client library
• leidenalg-0.8.10 Leiden is a general algorithm for methods of community detection in large networks.
• liac-arff-2.5.0 A module for read and write ARFF files in Python.
• libclang-14.0.1 Clang Python Bindings, mirrored from the official LLVM repo: https://github.com/llvm/llvm-project/tree/main/clang/bindings/python, to make the installation process easier.
• lief-0.12.1 Library to instrument executable formats
• lifelines-0.27.1 Survival analysis in Python, including Kaplan Meier, Nelson Aalen and regression
• linear-tsv-1.1.0 Line-oriented, tab-separated value format
• llvmlite-0.38.1 lightweight wrapper around basic LLVM functionality
• locket-0.2.1 File-based locks for Python on Linux and Windows
• lockfile-0.12.2 Platform-independent file locking module
• logilab-common-1.9.7 collection of low-level Python packages and modules used by Logilab projects
• loompy-3.0.7 Work with Loom files for single-cell RNA-seq data
• louvain-0.7.1 louvain is a general algorithm for methods of community detection in large networks.
• lxml-4.9.1 Powerful and Pythonic XML processing library combining libxml2/libxslt with the ElementTree API.
• macholib-1.16 Mach-O header analysis and editing
• manhole-1.8.0 Manhole is in-process service that will accept unix domain socket connections and present the
• manuel-1.12.4 Manuel lets you build tested documentation.
• matplotlib-3.4.3 Python plotting package
• matplotlib-inline-0.1.2 Inline Matplotlib backend for Jupyter
• mccabe-0.7.0 McCabe checker, plugin for flake8
• memoized-property-1.0.3 A simple python decorator for defining properties that only run their fget function once
• messytables-0.15.2 Parse messy tabular data in various formats
• misopy-0.5.4 Mixture of Isoforms model (MISO) for isoform quantitation using RNA-Seq
• mistune-0.8.4 A sane Markdown parser with useful plugins and renderers
• mock-4.0.3 Rolling backport of unittest.mock for all Pythons
• monotonic-1.6 An implementation of time.monotonic() for Python 2 & < 3.3
• more-itertools-8.8.0 More routines for operating on iterables, beyond itertools
• mox3-1.1.0 Mock object framework for Python
• mpi4py-3.1.1 Python bindings for MPI
• mpld3-0.5.8 D3 Viewer for Matplotlib
• mpmath-1.2.1 Python library for arbitrary-precision floating-point arithmetic
• msgpack-1.0.1 MessagePack serializer
• msrest-0.7.1 AutoRest swagger generator Python client runtime.
• msrestazure-0.6.4 AutoRest swagger generator Python client runtime. Azure-specific module.
• multidict-6.0.2 multidict implementation
• multipledispatch-0.6.0 Multiple dispatch
• munch-2.5.0 A dot-accessible dictionary (a la JavaScript objects)
• mypy-0.961 Optional static typing for Python
• mypy_extensions-0.4.3 Experimental type system extensions for programs checked with the mypy typechecker.
• mypytools-0.1.15 A bundle of tools to make using mypy easier
• nanoget-1.16.1 Functions to extract information from Oxford Nanopore sequencing data and alignments.
• nanoplotter-1.10.0 Plotting functions of Oxford Nanopore sequencing data
• natsort-8.1.0 Simple yet flexible natural sorting in Python.
• nbclient-0.5.3 A client library for executing notebooks. Formerly nbconvert’s ExecutePreprocessor.
• nbconvert-6.4.0 Converting Jupyter Notebooks
• nbformat-5.1.3 The Jupyter Notebook format
• nbval-0.9.6 A py.test plugin to validate Jupyter notebooks
• ndg-httpsclient-0.5.1 Provides enhanced HTTPS support for httplib and urllib2 using PyOpenSSL
• neo4j-driver-4.4.5 Neo4j Bolt driver for Python
• nest-asyncio-1.5.5 Patch asyncio to allow nested event loops
• nest_asyncio-1.5.1 Patch asyncio to allow nested event loops
• netCDF4-1.6.0 Provides an object-oriented python interface to the netCDF version 4 library.
• netaddr-0.8.0 A network address manipulation library for Python
• netifaces-0.11.0 Portable network interface information.
• networkx-2.8.4 Python package for creating and manipulating graphs and networks
• nibabel-4.0.1 Access a multitude of neuroimaging data formats
• nltk-3.7 Natural Language Toolkit
• nmslib-2.1.1 Non-Metric Space Library (NMSLIB)
• nose-1.3.7 nose extends unittest to make testing easier
• nose-exclude-0.5.0 Exclude specific directories from nosetests runs.
• nose_warnings_filters-0.1.5 Allow to inject warning filters during nosetest.
• notebook-6.4.0 A web-based notebook environment for interactive computing
• novaclient-auth-secretkey-0.1 Authentication plugin for novaclient enabling API key and secret key
• npyscreen-4.10.5 Writing user interfaces without all that ugly mucking about in hyperspace
• numba-0.55.2 compiling Python code using LLVM
• numcodecs-0.10.0 A Python package providing buffer compression and transformation codecs for use in data storage and communication applications.
• numexpr-2.8.3 Fast numerical expression evaluator for NumPy
• numpy-1.21.3 NumPy is the fundamental package for array computing with Python.
• numpy_groupies-0.9.17 Optimised tools for group-indexing operations: aggregated sum and more.
• numpydoc-1.4.0 Sphinx extension to support docstrings in Numpy format
• oauth-1.0.1 Library for OAuth version 1.0a.
• oauthlib-3.2.0 A generic, spec-compliant, thorough implementation of the OAuth request-signing logic
• objgraph-3.5.0 Draws Python object reference graphs with graphviz
• olefile-0.46 Python package to parse, read and write Microsoft OLE2 files (Structured Storage or Compound Document, Microsoft Office)
• oncodrivefml-2.4.0 Identify signals of positive selection in somatic mutations
• ont-fast5-api-4.0.2 Oxford Nanopore Technologies fast5 API software
• opencv-python-4.6.0.66 Wrapper package for OpenCV python bindings.
• openpyxl-3.0.10 A Python library to read/write Excel 2010 xlsx/xlsm files
• openstackdocstheme-2.4.0 OpenStack Docs Theme
• openstacksdk-0.99.0 An SDK for building applications to work with OpenStack
• opt_einsum-3.3.0 Optimizing numpys einsum function
• orderedmultidict-1.0.1 Ordered Multivalue Dictionary
• os-brick-5.2.1 OpenStack Cinder brick library for managing local volume attaches
• os-client-config-2.1.0 OpenStack Client Configuation Library
• os-service-types-1.7.0 Python library for consuming OpenStack sevice-types-authority data
• os-testr-3.0.0 A testr wrapper to provide functionality for OpenStack projects
• os_diskconfig_python_novaclient_ext-0.1.3 Disk Config extension for python-novaclient
• os_networksv2_python_novaclient_ext-0.26 Adds rackspace networks support to python-novaclient
• os_virtual_interfacesv2_python_novaclient_ext-0.20 Adds Virtual Interfaces support to python-novaclient
• osc-lib-2.6.0 OpenStackClient Library
• oscpy-0.6.0 A modern and efficient OSC Client/Server implementation
• oslo.concurrency-4.5.1 Oslo Concurrency library
• oslo.config-9.0.0 Oslo Configuration API
• oslo.context-5.0.0 Oslo Context library
• oslo.db-12.0.0 Oslo Database library
• oslo.i18n-5.1.0 Oslo i18n library
• oslo.log-5.0.0 oslo.log library
• oslo.privsep-3.0.0 OpenStack library for privilege separation
• oslo.serialization-5.0.0 Oslo Serialization library
• oslo.service-3.0.0 oslo.service library
• oslo.utils-6.0.0 Oslo Utility library
• oslosphinx-4.18.0 OpenStack Sphinx Extensions and Theme
• oslotest-4.5.0 Oslo test framework
• packaging-21.3 Core utilities for Python packages
• pandas-1.3.4 Powerful data structures for data analysis, time series, and statistics
• pandocfilters-1.5.0 Utilities for writing pandoc filters in python
• paramiko-2.7.2 SSH2 protocol library
• parse-1.19.0 parse() is the opposite of format()
• parso-0.8.2 A Python Parser
• partd-1.2.0 Appendable key-value storage
• pastel-0.2.1 Bring colors to your terminal.
• path-16.4.0 A module wrapper for os.path
• path.py-12.5.0 A module wrapper for os.path
• pathlib2-2.3.6 Object-oriented filesystem paths
• pathspec-0.9.0 Utility library for gitignore style pattern matching of file paths.
• patsy-0.5.2 A Python package for describing statistical models and for building design matrices.
• pauvre-0.2.3 Tools for plotting Oxford Nanopore and other long-read data.
• paycheck-1.0.2 A Python QuickCheck implementation
• pbr-5.6.0 Python Build Reasonableness
• pdm-pep517-1.0.4 A PEP 517 backend for PDM that supports PEP 621 metadata
• pefile-2022.5.30 Python PE parsing module
• pep517-0.12.0 Wrappers to build Python packages using PEP 517 hooks
• persistent-4.9.0 Translucent persistent objects
• pexpect-4.8.0 Pexpect allows easy control of interactive console applications.
• pickleshare-0.7.5 Tiny ‘shelve’-like database with concurrency support
• pifpaf-3.1.5 Suite of tools and fixtures to manage daemons for testing
• pigar-1.0.0 A fantastic tool to generate requirements for your Python project, and more than that.
• pip-21.2.2 The PyPA recommended tool for installing Python packages.
• pip_api-0.0.29 An unofficial, importable pip API
• pip_shims-0.7.3 Compatibility shims for pip versions 8 thru current.
• pipenv-2022.7.4 Python Development Workflow for Humans.
• pipreqs-0.4.11 Pip requirements.txt generator based on imports in project
• pkginfo-1.7.1 Query metadatdata from sdists / bdists / installed packages.
• plac-1.3.5 The smartest command line arguments parser in the world
• platformdirs-2.2.0 A small Python module for determining appropriate platform-specific dirs, e.g. a “user data dir”.
• plette-0.2.3 Structured Pipfile and Pipfile.lock models.
• plotly-5.9.0 An open-source, interactive data visualization library for Python
• plotsr 0.5.4
• pluggy-0.13.1 plugin and hook calling mechanisms for python
• ply-3.11 Python Lex & Yacc
• poetry-1.1.7 Python dependency management and packaging made easy.
• poetry-core-1.0.3 Poetry PEP 517 Build Backend
• pooch-1.5.2 “Pooch manages your Python library’s sample data files: it automatically downloads and stores them in a local directory, with support for versioning and corruption checks.”
• positional-1.2.1 Library to enforce positional or key-word arguments (deprecated/unmaintained)
• presto-0.7.0 A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data.
• pretend-1.0.9 A library for stubbing in Python
• prettytable-3.3.0 A simple Python library for easily displaying tabular data in a visually appealing ASCII table format
• process-tests-2.1.2 Tools for testing processes.
• profilehooks-1.12.0 Decorators for profiling/timing/tracing individual functions
• progressbar33-2.4 Text progress bar library for Python.
• prometheus_client-0.11.0 Python client for the Prometheus monitoring system.
• prompt_toolkit-3.0.19 Library for building powerful interactive command lines in Python
• protobuf-4.21.2
• prov-2.0.0 A library for W3C Provenance Data Model supporting PROV-JSON, PROV-XML and PROV-O (RDF)
• psutil-5.8.0 Cross-platform lib for process and system monitoring in Python.
• psycopg2-2.9.3 psycopg2 - Python-PostgreSQL Database Adapter
• ptyprocess-0.7.0 Run a subprocess in a pseudo terminal
• pure-eval-0.2.2 Safely evaluate AST nodes without side effects
• purl-1.6 An immutable URL class for easy URL-building and manipulation
• py-1.10.0 library with cross-python path, ini-parsing, io, code, log facilities
• py-cpuinfo-8.0.0 Get CPU info with pure Python 2 & 3
• py2bit-0.3.0 A package for accessing 2bit files using lib2bit
• py4j-0.10.9.5 Enables Python programs to dynamically access arbitrary Java objects
• pyArango-2.0.1 An easy to use python driver for ArangoDB with built-in validation
• pyBigWig-0.3.18 A package for accessing bigWig files using libBigWig
• pyFFTW-0.13.0 A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms.
• pyOpenSSL-22.0.0 Python wrapper module around the OpenSSL library
• py_expression_eval-0.3.13 Python Mathematical Expression Evaluator
• pyasn1-0.4.8 ASN.1 types and codecs
• pyasn1-modules-0.2.8 A collection of ASN.1-based protocols modules.
• pybedtools 0.8.2 Module
• pybind11-2.9.2 Seamless operability between C++11 and Python
• pyblake2-1.1.2 BLAKE2 hash function extension module
• pycares-4.2.1 Python interface for c-ares
• pycodestyle-2.8.0 Python style guide checker
• pycosat-0.6.3 bindings to picosat (a SAT solver)
• pycparser-2.20 C parser in Python
• pycrypto-2.6.1 Cryptographic modules for Python.
• pycryptodome-3.15.0 Cryptographic library for Python
• pycurl-7.45.1 PycURL – A Python Interface To The cURL library
• pydicom-2.3.0 A pure Python package for reading and writing DICOM data
• pydocstyle-6.1.1 Python docstring style checker
• pydot-1.4.2 Python interface to Graphviz’s Dot
• pyem-2.1.0 Project-level Python virtual environment management tool.
• pyemd-0.5.1 A Python wrapper for Ofir Pele and Michael Werman’s implementation of the Earth Mover’s Distance.
• pyensembl-2.0.0 Python interface to ensembl reference genome metadata
• pyerfa-2.0.0.1 Python bindings for ERFA
• pyfaidx-0.7.0 pyfaidx: efficient pythonic random access to fasta subsequences
• pyfastaq-3.17.0 Script to manipulate FASTA and FASTQ files, plus API for developers
• pyflakes-2.4.0 passive checker of Python programs
• pygithub3-0.5.1 Python wrapper for the github v3 api
• pyinotify-0.9.6 Linux filesystem events monitoring
• pyinstaller-5.2 PyInstaller bundles a Python application and all its dependencies into a single package.
• pyinstaller-hooks-contrib-2022.8 Community maintained hooks for PyInstaller
• pykerberos-1.2.4 High-level interface to Kerberos
• pylev-1.4.0 A pure Python Levenshtein implementation that’s not freaking GPL’d.
• pylint-2.14.4 python code static checker
• pymongo-4.1.1 Python driver for MongoDB http://www.mongodb.org
• pymssql-2.2.5 DB-API interface to Microsoft SQL Server for Python. (new Cython-based version)
• pymummer-0.11.0 Wrapper for MUMmer
• pynast-1.2.2 The Python Nearest Alignment Space Termination tool
• pynndescent-0.5.7 Nearest Neighbor Descent
• pypandoc-1.8.1 Thin wrapper for pandoc.
• pyparsing-3.0.9 pyparsing module - Classes and methods to define and execute parsing grammars
• pyperclip-1.8.2 A cross-platform clipboard module for Python. (Only handles plain text for now.)
• pyro-api-0.1.2 Generic API for dispatch to Pyro backends.
• pyro-ppl-1.8.1 A Python library for probabilistic modeling and inference
• pyrsistent-0.18.0 Persistent/Functional/Immutable data structures
• pysam-0.19.1 pysam
• pyserial-3.5 Python Serial Port Extension
• pyspnego-0.5.4 Windows Negotiate Authentication Client and Server
• pytest-6.2.4 pytest: simple powerful testing with Python
• pytest-checkdocs-2.7.1 check the README when running tests
• pytest-cov-3.0.0 Pytest plugin for measuring coverage.
• pytest-flake8-1.1.1 pytest plugin to check FLAKE8 requirements
• pytest-mock-3.8.2 Thin-wrapper around the mock package for easier use with pytest
• python-Levenshtein-0.12.2 Python extension for computing string edit distances and similarities.
• python-cinderclient-8.3.0 OpenStack Block Storage API Client Library
• python-consul-1.1.0 Python client for Consul (http://www.consul.io/)
• python-dateutil-2.8.2 Extensions to the standard Python datetime module
• python-dotenv-0.20.0 Read key-value pairs from a .env file and set them as environment variables
• python-editor-1.0.4 Programmatically open an editor, capture the result.
• python-freezerclient-4.4.0 OpenStack Disaster Recovery API Client Library
• python-glanceclient-4.0.1 OpenStack Image API Client Library
• python-hostlist-1.21 Python module for hostlist handling
• python-igraph 0.9.8 Module
• python-json-logger-2.0.4 A python library adding a json log formatter
• python-keystoneclient-4.5.0 Client Library for OpenStack Identity
• python-neutronclient-7.8.0 CLI and Client Library for OpenStack Networking
• python-novaclient-18.0.0 Client library for OpenStack Compute API
• python-openstackclient-5.8.0 OpenStack Command-line Client
• python-pam-2.0.2 Python PAM module using ctypes, py3
• python-snappy-0.6.1 Python library for the snappy compression library from Google
• python-subunit-1.4.0 Python implementation of subunit test streaming protocol
• python-swiftclient-4.0.0 OpenStack Object Storage API Client Library
• pythran-0.10.0 Ahead of Time compiler for numeric kernels
• pytoml-0.1.21 A parser for TOML-0.4.0
• pytoolconfig-1.2.1 Python tool configuration
• pytype-2022.6.30 Python type inferencer
• pytz-2021.1 World timezone definitions, modern and historical
• pytz-deprecation-shim-0.1.0.post0 Shims to make deprecation of pytz easier
• pyxdg-0.28 PyXDG contains implementations of freedesktop.org standards in python.
• pyzmq-22.2.1 Python bindings for 0MQ
• qrcode-7.3.1 QR Code image generator
• rackspace-auth-openstack-1.3 Rackspace Auth Plugin for OpenStack Clients.
• rackspace-novaclient-2.1 Metapackage to install python-novaclient and Rackspace extensions
• ratelimiter-1.2.0.post0 Simple python rate limiting object
• rax_default_network_flags_python_novaclient_ext-0.4.0 Novaclient Extension for Instance Default Network Flags
• rax_scheduled_images_python_novaclient_ext-0.3.1 Extends python-novaclient to use RAX-SI, the Rackspace Nova API Scheduled Images extension
• rdflib-6.1.1 RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information.
• rdflib-jsonld-0.6.2 rdflib extension adding JSON-LD parser and serializer
• readme_renderer-35.0 readme_renderer is a library for rendering “readme” descriptions for Warehouse
• redis-4.3.4 Python client for Redis database and key-value store
• regex-2021.8.3 Alternative regular expression module, to replace re.
• reno-3.5.0 RElease NOtes manager
• reportlab-3.6.11 The Reportlab Toolkit
• repoze.lru-0.7 A tiny LRU cache implementation and decorator
• repoze.sphinx.autointerface-1.0.0 Sphinx extension: auto-generates API docs from Zope interfaces
• requests-2.26.0 Python HTTP for Humans.
• requests-kerberos-0.14.0 A Kerberos authentication handler for python-requests
• requests-mock-1.9.3 Mock out responses from the requests package
• requests-oauthlib-1.3.1 OAuthlib authentication support for Requests.
• requests-toolbelt-0.9.1 A utility belt for advanced users of python-requests
• requestsexceptions-1.4.0 Import exceptions from potentially bundled packages in requests.
• requirementslib-1.6.7 A tool for converting between pip-style and pipfile requirements.
• resolvelib-0.8.1 Resolve abstract dependencies into concrete ones
• restructuredtext-lint-1.4.0 reStructuredText linter
• rethinkdb-2.4.9 Python driver library for the RethinkDB database server.
• retry-0.9.2 Easy to use retry decorator.
• retrying-1.3.3 Retrying
• retype-21.12.0 re-apply types from .pyi stub files to your codebase
• rfc3986-2.0.0 Validating URI References per RFC 3986
• rfc3987-1.3.8 Parsing and validation of URIs (RFC 3986) and IRIs (RFC 3987)
• rich-12.5.1 Render rich text, tables, progress bars, syntax highlighting, markdown and more to the terminal
• roman-3.3 Integer to Roman numerals converter
• rsa-4.8 Pure-Python RSA implementation
• ruamel.yaml-0.17.21 ruamel.yaml is a YAML parser/emitter that supports roundtrip preservation of comments, seq/map flow style, and map key order
• ruffus-2.8.4 Light-weight Python Computational Pipeline Management
• s3fs-2022.5.0 Convenient Filesystem interface over S3
• s3transfer-0.6.0 An Amazon S3 Transfer Manager
• scandir-1.10.0 scandir, a better directory iterator and faster os.walk()
• scanpy-1.9.1 Single-Cell Analysis in Python.
• schema-salad-8.3.20220626185350 Schema Annotations for Linked Avro Data (SALAD)
• sci-0.1.7 a collection of convenience and wrapper functions supporting tasks frequently needed by scientists
• scikit-bio-0.5.7 Data structures, algorithms and educational resources for bioinformatics.
• scikit-build-0.11.1 Improved build system generator for Python C/C++/Fortran/Cython extensions
• scikit-image-0.19.1 Image processing in Python
• scikit-learn 1.0.1 Module
• scikit-misc-0.1.4 Miscellaneous tools for scientific computing.
• scikit-optimize 0.9.0 Module
• scipy-1.7.1 SciPy: Scientific Library for Python
• scvi-0.6.8 Single-cell Variational Inference
• seaborn-0.11.2 seaborn: statistical data visualization
• selectors34-1.2 Backport of the selectors module from Python 3.4.
• selenium-3.141.0
• semantic_version-2.8.5 A library implementing the ‘SemVer’ scheme.
• serializable-0.2.1 Base class with serialization helpers for user-defined Python objects
• serpent-1.41 Serialization based on ast.literal_eval
• service-identity-21.1.0 Service identity verification for pyOpenSSL & cryptography.
• session-info-1.0.0 session_info outputs version information for modules loaded in the current session, Python, and the OS.
• setuptools-57.4.0 Easily download, build, install, upgrade, and uninstall Python packages
• setuptools-git-1.2 Setuptools revision control system plugin for Git
• setuptools-rust-0.12.1 Setuptools Rust extension plugin
• setuptools_scm-6.0.1 the blessed package to manage your versions by scm tags
• sh-1.14.2 Python subprocess replacement
• shap-0.41.0 A unified approach to explain the output of any machine learning model.
• shellescape-3.8.1 Shell escape a string to safely use it as a token in a shell command (backport of cPython shlex.quote for Python versions 2.x & < 3.3)
• shellingham-1.4.0 Tool to Detect Surrounding Shell
• 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-3.17.3 Simple, fast, extensible JSON encoder/decoder for Python
• sinfo-0.3.4 sinfo outputs version information for modules loaded in the current session, Python, and the OS.
• singledispatch-3.7.0 Backport functools.singledispatch from Python 3.4 to Python 2.6-3.3.
• singularity-cli-0.1.10 Opinionated CLI for Singularity PAAS
• sip-6.6.2 A Python bindings generator for C/C++ libraries
• six-1.16.0 Python 2 and 3 compatibility utilities
• slicer-0.0.7 A small package for big slicing.
• slurm-pipeline-4.0.13 A Python class and utility script for scheduling SLURM jobs
• slurmpy-0.0.8 submit jobs to slurm with python
• smart-open-6.0.0 Utils for streaming large files (S3, HDFS, GCS, Azure Blob Storage, gzip, bz2…)
• smmap-5.0.0 A pure Python implementation of a sliding window memory map manager
• smmap2-3.0.1 A mirror package for smmap
• snakemake-7.8.5 Snakemake is a workflow management system that aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern specification language in python style. Snakemake workflows are essentially Python scripts extended by declarative code to define rules. Rules describe how to create output files from input files.
• sniffio-1.2.0 Sniff out which async library your code is running under
• snowballstemmer-2.1.0 This package provides 29 stemmers for 28 languages generated from Snowball algorithms.
• softlayer_messaging-1.0.3 SoftLayer Message Queue Client
• sortedcontainers-2.4.0 Sorted Containers – Sorted List, Sorted Dict, Sorted Set
• soupsieve-2.3.2.post1 A modern CSS selector implementation for Beautiful Soup.
• sphinx-argparse-0.3.1 A sphinx extension that automatically documents argparse commands and options
• sphinx-autodoc-typehints-1.18.3 Type hints (PEP 484) support for the Sphinx autodoc extension
• sphinx-bootstrap-theme-0.7.1 Sphinx Bootstrap Theme.
• sphinx-rtd-theme-1.0.0 Read the Docs theme for Sphinx
• sphinxcontrib-applehelp-1.0.2 sphinxcontrib-applehelp is a sphinx extension which outputs Apple help books
• sphinxcontrib-devhelp-1.0.2 sphinxcontrib-devhelp is a sphinx extension which outputs Devhelp document.
• sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-htmlhelp is a sphinx extension which renders HTML help files
• sphinxcontrib-jsmath-1.0.1 A sphinx extension which renders display math in HTML via JavaScript
• sphinxcontrib-programoutput-0.17 Sphinx extension to include program output
• sphinxcontrib-qthelp-1.0.3 sphinxcontrib-qthelp is a sphinx extension which outputs QtHelp document.
• sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-serializinghtml is a sphinx extension which outputs “serialized” HTML files (json and pickle).
• sphinxcontrib-websupport-1.2.4 Sphinx API for Web Apps
• sphinxcontrib_github_alt-1.2 Link to GitHub issues, pull requests, commits and users from Sphinx docs.
• sqlalchemy-migrate-0.13.0 Database schema migration for SQLAlchemy
• sqlparse-0.4.2 A non-validating SQL parser.
• ssh-import-id-5.11 Authorize SSH public keys from trusted online identities
• stack-data-0.3.0 Extract data from python stack frames and tracebacks for informative displays
• statsmodels-0.13.1 Statistical computations and models for Python
• stdeb-0.10.0 Python to Debian source package conversion utility
• stdlib-list-0.8.0 A list of Python Standard Libraries (2.6-7, 3.2-9).
• stestr-3.2.1 A parallel Python test runner built around subunit
• stevedore-4.0.0 Manage dynamic plugins for Python applications
• stopit-1.1.2 Timeout control decorator and context managers, raise any exception in another thread
• stor-4.0.2 Cross-compatible API for accessing Posix and OBS storage systems
• strict-rfc3339-0.7 Strict, simple, lightweight RFC3339 functions
• stuf-0.9.16 Normal, default, ordered, chained, restricted, counter, and frozen dictionaries with attribute-style access.
• subunit2sql-1.10.0 Command to Read a subunit file or stream and put the data in a SQL DB
• swiftly-2.06 Command line tool and client bindings for OpenStack Swift.
• sybil-3.0.1 Automated testing for the examples in your code and documentation.
• sympy-1.10.1 Computer algebra system (CAS) in Python
• synapseclient-2.6.0 A client for Synapse, a collaborative compute space that allows scientists to share and analyze data together.
• tables-3.7.0 Hierarchical datasets for Python
• tabulate-0.8.9 Pretty-print tabular data
• tabulator-1.53.5 Consistent interface for stream reading and writing tabular data (csv/xls/json/etc)
• tblib-1.7.0 Traceback serialization library.
• tenacity-8.0.1 Retry code until it succeeds
• termcolor-1.1.0 ANSII Color formatting for output in terminal.
• terminado-0.10.1 Tornado websocket backend for the Xterm.js Javascript terminal emulator library.
• testfixtures-7.0.0 A collection of helpers and mock objects for unit tests and doc tests.
• testpath-0.5.0 Test utilities for code working with files and commands
• testrepository-0.0.20 A repository of test results.
• testresources-2.0.1 Testresources, a pyunit extension for managing expensive test resources
• testscenarios-0.5.0 Testscenarios, a pyunit extension for dependency injection
• testtools-2.5.0 Extensions to the Python standard library unit testing framework
• textblob-0.17.1 Simple, Pythonic text processing. Sentiment analysis, part-of-speech tagging, noun phrase parsing, and more.
• texttable-1.6.4 module for creating simple ASCII tables
• threadpoolctl-2.2.0 threadpoolctl
• tifffile-2021.11.2 Read and write TIFF files
• tinycss2-1.1.1 A tiny CSS parser
• tokenize-rt-4.2.1 A wrapper around the stdlib tokenize which roundtrips.
• toml-0.10.2 Python Library for Tom’s Obvious, Minimal Language
• tomli-2.0.1 A lil’ TOML parser
• tomlkit-0.7.2 Style preserving TOML library
• toolz-0.12.0 List processing tools and functional utilities
• toposort-1.7 “Implements a topological sort algorithm.”
• torch-1.12.0 Tensors and Dynamic neural networks in Python with strong GPU acceleration
• torchfile-0.1.0 Torch7 binary serialized file parser
• tornado-6.1 Tornado is a Python web framework and asynchronous networking library, originally developed at FriendFeed.
• tqdm-4.64.0 Fast, Extensible Progress Meter
• traitlets-5.0.5
• treq-22.2.0 High-level Twisted HTTP Client API
• tslearn-0.5.2 A machine learning toolkit dedicated to time-series data
• tslib-1.6 A library for dealing with human-readable time offsets and timestamps
• twine-4.0.1 Collection of utilities for publishing packages on PyPI
• twobitreader-3.1.7 A fast python package for reading .2bit files (used by the UCSC genome browser)
• typechecks-0.1.0 Helper functions for runtime type checking
• typed-ast-1.5.4 a fork of Python 2 and 3 ast modules with type comment support
• typing-extensions-4.3.0 Backported and Experimental Type Hints for Python 3.7+
• typing_extensions-3.10.0.0 Backported and Experimental Type Hints for Python 3.7+
• typing_inspect-0.7.1 Runtime inspection utilities for typing module.
• tzdata-2022.1 Provider of IANA time zone data
• tzlocal-4.2 tzinfo object for the local timezone
• ujson-4.0.2 Ultra fast JSON encoder and decoder for Python
• umap-learn-0.5.3 Uniform Manifold Approximation and Projection
• umi_tools-1.1.2 umi_tools: Tools for UMI analyses
• 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-4.1.1 Implementation of RFC 6570 URI Templates
• urllib3-1.26.6 HTTP library with thread-safe connection pooling, file post, and more.
• urwid-2.1.2 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.
• vine-5.0.0 Promises, promises, promises.
• virtualenv-20.7.0 Virtual Python Environment builder
• virtualenv-clone-0.5.7 script to clone virtualenvs.
• visdom-0.1.8.9 A tool for visualizing live, rich data for Torch and Numpy
• visitor-0.1.3 A tiny pythonic visitor implementation.
• vistir-0.5.2 Miscellaneous utilities for dealing with filesystems, paths, projects, subprocesses, and more.
• voluptuous-0.13.1
• wadllib-1.3.6 Navigate HTTP resources using WADL files as guides.
• warlock-2.0.1 Python object model built on JSON schema and JSON patch.
• watchdog-2.1.9 Filesystem events monitoring
• wcwidth-0.2.5 Measures the displayed width of unicode strings in a terminal
• webcolors-1.12 A library for working with color names and color values formats defined by HTML and CSS.
• webencodings-0.5.1 Character encoding aliases for legacy web content
• websocket-0.2.1 Websocket implementation for gevent
• whatshap-1.4 phase genomic variants using DNA sequencing reads
• wheel-0.36.2 A built-package format for Python
• widgetsnbextension-3.5.1 Jupyter interactive widgets for Jupyter Notebook
• wrapt-1.14.1 Module for decorators, wrappers and monkey patching.
• xattr-0.9.9 Python wrapper for extended filesystem attributes
• xlrd-2.0.1 Library for developers to extract data from Microsoft Excel (tm) .xls spreadsheet files
• xlwt-1.3.0 Library to create spreadsheet files compatible with MS Excel 97/2000/XP/2003 XLS files, on any platform, with Python 2.6, 2.7, 3.3+
• xmlschema-1.11.3 An XML Schema validator and decoder
• xopen-1.5.0 Open compressed files transparently
• yagdspy-1.0 Graph dependancy system for processing tasks
• yamlordereddictloader-0.4.0 YAML loader and dump for PyYAML allowing to keep keys order.
• yappi-1.3.5 Yet Another Python Profiler
• yarg-0.1.9 A semi hard Cornish cheese, also queries PyPI (PyPI client)
• yarl-1.7.2 Yet another URL library
• yaspin-2.1.0 Yet Another Terminal Spinner
• yte-1.5.1 A YAML template engine with Python expressions
• zappy-0.2.0 Distributed processing with NumPy and Zarr.
• zarr-2.12.0 An implementation of chunked, compressed, N-dimensional arrays for Python.
• zict-2.0.0 Mutable mapping tools
• zipfile36-0.1.3 Read and write ZIP files - backport of the zipfile module from Python 3.6
• zipp-3.5.0 Backport of pathlib-compatible object wrapper for zip files
• zope.component-5.0.1 Zope Component Architecture
• zope.configuration-4.4.1 Zope Configuration Markup Language (ZCML)
• zope.copy-4.2 Pluggable object copying mechanism
• zope.deferredimport-4.4 zope.deferredimport allows you to perform imports names that will only be resolved when used in the code.
• zope.deprecation-4.4.0 Zope Deprecation Infrastructure
• zope.event-4.5.0 Very basic event publishing system
• zope.exceptions-4.5 Zope Exceptions
• zope.hookable-5.1.0 Zope hookable
• zope.i18nmessageid-5.0.1 Message Identifiers for internationalization
• zope.interface-5.4.0 Interfaces for Python
• zope.location-4.2 Zope Location
• zope.proxy-4.5.0 Generic Transparent Proxies
• zope.schema-6.2.0 zope.interface extension for defining data schemas
• zope.security-5.3 Zope Security Framework
• zope.testing-4.10 Zope testing helpers
• zope.testrunner-5.5 Zope testrunner script.
• zstandard-0.18.0 Zstandard bindings for Python