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Overview of Python Packages for Scientific Computing
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Overview of Python Packages for Scientific Computing
Resources
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The Python Package Index (PyPI) is a repository of software for the Python programming language.
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NumFOCUS is a nonprofit that supports open source scientific computing.
Courses
| Course | Description |
|---|---|
| Software Carpentry | Introduction to various programming topics |
| Data carpentry | Hands-on, interactive lessons on various data analysis topics |
| Intro to Data Analysis | Free Udacity course on using NumPy and Pandas for data analysis |
| DataCamp, Dataquest | Courses on various data science topics (not all are free) |
Notebooks
| Package | Description |
|---|---|
| Jupyter | Create and share documents that contain live code, equations, visualizations and explanatory text |
| nteract | Embeds Jupyter notebooks as a desktop application |
Data Wrangling
| Package | Description |
|---|---|
| pandas | Offers table-like structure and some analysis tools |
Plotting and Visualisation
| Package | Description |
|---|---|
| matplotlib | The standard library for generating plots |
| seaborn | High-level interface to matplotlib based on pandas |
| bokeh, Plotly | Creates interactive visualisations for the web |
Bioinformatics
| Package | Description |
|---|---|
| scikit-bio | Bioinformatics algorithms in Python |
Machine Learning
| Package | Description |
|---|---|
| scikit-learn | The standard machine learning library |
| Orange | Application for interactive data analysis |
| statsmodels | Statistical models and tests |
Deep Learning
| Package | Description |
|---|---|
| TensorFlow | Neural network library from Google |
| Theano | Another neural network library |
| Lasagne | High-level interface to Theano |
Networks and Graphs
| Package | Description |
|---|---|
| NetworkX | Create, manipulate and anaylse networks and graphs |
| NetworKit | Large-sale network analysis |
Image Processing
| Package | Description |
|---|---|
| scikit-image | Collection of algorithms for image processing |
| OpenCV | Computational efficient library for computer vision with Python interface |
| Simple ITK | Library for medical image processing |
Natural Language Processing (NLP)
| Package | Description |
|---|---|
| SpaCy | Library with lots of NLP algorithms |
| gensim | Topic modelling |
Bayesian Inference
| Package | Description |
|---|---|
| Stan | Statistical modeling, data analysis, and prediction in the Bayesian world |
| PyMC3 | Alternative package for Bayesian statistical modeling |
Survival Analysis
| Package | Description |
|---|---|
| lifelines | Survival analysis in Python |
| scikit-survival | Survival analysis based on top of scikit-learn |
Mathematics
| Package | Description |
|---|---|
| scipy | statistics, linear algebra, numerical integration and optimisation |
| sympy | Library for symbolic mathematics |
| cvxpy, cvxopt | Convex optimisation |
| FEniCS | Platform for partial differential equations (PDE) |
Workflow
| Package | Description |
|---|---|
| Luigi | Platform from Spotify to build complex pipelines |
| Airflow | Another platform for managing workflows |
| Dask | Parallel computing library |
| IPython Parallel | Parallel processing built on top of IPython |
Performance Improvement
| Package | Description |
|---|---|
| Cython | Translates Python-style code to C |
| Numba | Generates optimised code using a just-in-time compiler |
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