Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.
GSEApy is a Python/Rust implementation for GSEA and wrapper for Enrichr. GSEApy can be used for RNA-seq, ChIP-seq, Microarray data. It can be used for convenient GO enrichment and to produce publication quality figures in Python.
Spglib is a library for finding and handling crystal symmetries written in C. This package provides Python bindings for spglib, allowing Python programs to find symmetry operations, identify space groups, and perform other symmetry-related operations on crystal structures.
warcio is a Python library to read and write the WARC format commonly used in Web archives. It is designed for fast, low-level access to web archival content, oriented around a stream of WARC records rather than files.
Joblib is a set of tools to provide lightweight pipelining in Python. In particular, joblib offers: transparent disk-caching of the output values and lazy re-evaluation (memoize pattern), easy simple parallel computing logging and tracing of the execution.
cattrs is an Python library for structuring and unstructuring data. cattrs works best with attrs classes, dataclasses and the usual Python collections, but other kinds of classes can also be supported by manually registering converters.
k5test is a library for setting up self-contained Kerberos 5 environments, and running Python unit tests inside those environments. It is based on the file of the same name found alongside the MIT Kerberos 5 unit tests.
Pyface contains toolkit-independent GUI abstraction layers, used to support the TraitsUI package. Thus, you can write code in the abstraction of the Pyface API and the selected toolkit and backend take care of the details of displaying them.
This package implements a variety of persistent homology algorithms. It provides an interface for
computing persistence cohomology of sparse and dense data sets
visualizing persistence diagrams
computing lowerstar filtrations on images
computing representative cochains
Shiver (Spectroscopy Histogram Visualizer for Event Reduction) is a desktop application for examining Time of Flight inelastic neutron data from single crystal, direct geometry experiments. It integrates with Mantid Workbench and appears in the Interfaces menu when both packages are installed.
Bcrypt is a Python module which provides a password hashing method based on the Blowfish password hashing algorithm, as described in "A Future-Adaptable Password Scheme" by Niels Provos and David Mazieres.
Scrapy is a fast high-level web crawling and web scraping framework, used to crawl websites and extract structured data from their pages. It can be used for a wide range of purposes, from data mining to monitoring and automated testing.
Provides a high-level interface to the ECWMF ECCODES C library for reading GRIB files. There are limited capabilities for writing GRIB files (you can modify the contents of an existing file, but you can't create one from scratch).
This package provides a set of helpers for matplotlib to more easily produce plots typically needed in HEP as well as style them in way that's compatible with current collaboration requirements (ROOT-like plots for CMS, ATLAS, LHCb, ALICE).
Stanza is a collection of accurate and efficient tools for the linguistic analysis of many human languages. Starting from raw text, Stanza divides it into sentences and words, and then can recognize parts of speech and entities, do syntactic analysis, and more.
asprin is a general framework for optimization in ASP, that allows for computing optimal stable models of logic programs by means of preferences. Some preference types are already predefined, but more can be added as logic programs.
psleak is a testing framework for detecting memory leaks and unclosed resources created by Python functions, particularly those implemented in C extensions.
It was originally developed as part of psutil test suite, and later split out into a standalone project.
This package provides access to the Stripe financial services' API. It includes a pre-defined set of classes for API resources that initialize themselves dynamically from API responses which makes it compatible with a wide range of versions of the Stripe API.
Orjson is a fast, correct JSON library for Python. It benchmarks as the fastest Python library for JSON and is more correct than the standard json library or other third-party libraries. It serializes dataclass, datetime, numpy, and UUID instances natively.
Pifpaf is a suite of fixtures and a command-line tool that starts and stops daemons for a quick throw-away usage. This is typically useful when needing these daemons to run integration testing. It originally evolved from its precursor overtest.
NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities.
pybids provides a set of tools for working with BIDS datasets. The BIDS standard aims at organizing and describing neuroimaging data in a uniform way in order to facilitate data sharing within the scientific community.
Carbon is a backend data caching and persistence daemon for Graphite. Carbon is responsible for receiving metrics over the network, caching them in memory for "hot queries" from the Graphite-Web application, and persisting them to disk using the Whisper time-series library.
Vector is a Python library for 2D and 3D spatial vectors, as well as 4D space-time vectors. It is especially intended for performing geometric calculations on arrays of vectors, rather than one vector at a time in a Python for loop.