Bioinformatics-Guide

Bioinformatics Guide
https://github.com/mikeroyal/Bioinformatics-Guide

Last synced: 1 day ago
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Tools
- Mockito
- SpotBugs
- Java SE
- JDK Development Tools
- IntelliJ IDEA
- NetBeans
- Elasticsearch
- RxJava - based programs by using observable sequences. It extends the [observer pattern](http://en.wikipedia.org/wiki/Observer_pattern) to support sequences of data/events and adds operators that allow you to compose sequences together declaratively while abstracting away concerns about things like low-level threading, synchronization, thread-safety and concurrent data structures.
- Guava
- Retrofit - safe HTTP client for Android and Java develped by Square.
- Apache Spark - scale data processing. It provides high-level APIs in Scala, Java, Python, and R, and an optimized engine that supports general computation graphs for data analysis. It also supports a rich set of higher-level tools including Spark SQL for SQL and DataFrames, MLlib for machine learning, GraphX for graph processing, and Structured Streaming for stream processing.
- Apache Flink - and batch-processing capabilities with elegant and fluent APIs in Java and Scala.
- Fastjson
- libGDX - platform Java game development framework based on OpenGL (ES) that works on Windows, Linux, Mac OS X, Android, your WebGL enabled browser and iOS.
- Jenkins - source automation server. Built with Java, it provides over 1700 [plugins](https://plugins.jenkins.io/) to support automating virtually anything, so that humans can actually spend their time doing things machines cannot.
- DBeaver - platform database tool for developers, SQL programmers, database administrators and analysts. Supports any database which has JDBC driver (which basically means - ANY database). EE version also supports non-JDBC datasources (MongoDB, Cassandra, Redis, DynamoDB, etc).
- Redisson - Memory Data Grid. Over 50 Redis based Java objects and services: Set, Multimap, SortedSet, Map, List, Queue, Deque, Semaphore, Lock, AtomicLong, Map Reduce, Publish / Subscribe, Bloom filter, Spring Cache, Tomcat, Scheduler, JCache API, Hibernate, MyBatis, RPC, and local cache.
- GraalVM - based languages like Java, Scala, Clojure, Kotlin, and LLVM-based languages such as C and C++.
- Gradle - language software development. From mobile apps to microservices, from small startups to big enterprises, Gradle helps teams build, automate and deliver better software, faster. Write in Java, C++, Python or your language of choice.
- Apache Groovy - typing and static compilation capabilities, for the Java platform aimed at improving developer productivity thanks to a concise, familiar and easy to learn syntax. It integrates smoothly with any Java program, and immediately delivers to your application powerful features, including scripting capabilities, Domain-Specific Language authoring, runtime and compile-time meta-programming and functional programming.
- JaCoCo
- Apache JMeter
- Junit
- SpringBoot - powered, production-grade applications and services with absolute minimum fuss. It takes an opinionated view of the Spring platform so that new and existing users can quickly get to the bits they need.
- YourKit
- PHP - purpose scripting language that is especially suited to web development. Fast, flexible and pragmatic, PHP powers everything from your blog to the most popular websites in the world.
- PHP 8
- What's New in PHP 8 - Auth0
- PHP Manual
- MIT's PHP Code Style Guide
- PHP Style Guide
- PHP tutorial by W3Schools
- PHP MySQL & CodeIgniter Course on Udemy
- PhpStorm
- Laravel
- PHP Intelephense
- PHP Tools for Visual Studio/VS Code
- Symfony
- CakePHP
- Composer
- DesignPatternsPHP
- CodeIgniter
- HHVM - source virtual machine designed for executing programs written in [Hack](https://hacklang.org/). HHVM uses a just-in-time (JIT) compilation approach to achieve superior performance while maintaining amazing development flexibility. HHVM should be used together with a webserver like the built in, easy to deploy [Proxygen](https://docs.hhvm.com/hhvm/basic-usage/proxygen), or a [FastCGI-based](https://docs.hhvm.com/hhvm/advanced-usage/fastCGI) webserver on top of nginx or Apache.
- Phalcon
- Swoole - driven asynchronous & coroutine-based concurrency networking communication engine with high performance written in C and C++ for PHP.
- Matomo - featured PHP MySQL software program that you download and install on your own webserver. At the end of the five-minute installation process, you will be given a JavaScript code. Simply copy and paste this tag on websites you wish to track and access your analytics reports in real-time.
- Grav - based Web-platform. There is Zero installation required. Just extract the ZIP archive, and you are already up and running. It follows similar principles to other flat-file CMS platforms, but has a different design philosophy than most. Grav comes with a powerful Package Management System to allow for simple installation and upgrading of plugins and themes, as well as simple updating of Grav itself.
- Slim
- Java Design Patterns
- okhttp
- LeakCanary
MATLAB Learning Resources
MATLAB Tools
- MATLAB Online
- Simulink - Based Design. It supports simulation, automatic code generation, and continuous testing of embedded systems.
- Robotics Toolbox for MATLAB - holonomic vehicle. The Toolbox also including a detailed Simulink model for a quadrotor flying robot.
- hctsa - series analysis using Matlab.
- Plotly
- YALMIP
- GNU Octave - level interpreted language, primarily intended for numerical computations. It provides capabilities for the numerical solution of linear and nonlinear problems, and for performing other numerical experiments. It also provides extensive graphics capabilities for data visualization and manipulation.
- R
- An Introduction to R
- Google's R Style Guide
- R developer's guide to Azure
- Running R on AWS
- RStudio Server Pro for AWS
- Learn R by Codecademy
- Learn R Programming with Online Courses and Lessons by edX
- R Language Courses by Coursera
- Learn R For Data Science by Udacity
- RStudio - highlighting editor that supports direct code execution, and tools for plotting, history, debugging and workspace management.
- Shiny
- Plotly
- Metaflow - life data science projects. Metaflow was originally developed at Netflix to boost productivity of data scientists who work on a wide variety of projects from classical statistics to state-of-the-art deep learning.
- Prophet - linear trends are fit with yearly, weekly, and daily seasonality, plus holiday effects. It works best with time series that have strong seasonal effects and several seasons of historical data.
- LightGBM
- MLR
- CatBoost
- Plumber
- Drake - focused pipeline toolkit for reproducibility and high-performance computing.
- DiagrammeR
- Knitr - purpose literate programming engine in R, with lightweight API's designed to give users full control of the output without heavy coding work.
- Broom
- Shiny
- MATLAB Schemer
- LRSLibrary - Rank and Sparse Tools for Background Modeling and Subtraction in Videos. The library was designed for moving object detection in videos, but it can be also used for other computer vision and machine learning problems.
- SEA-MAT
- Gramm - level interface to produce publication-quality plots of complex data with varied statistical visualizations. Gramm is inspired by R's ggplot2 library.
- Rplugin
- ML workspace - in-one web-based IDE specialized for machine learning and data science. It is simple to deploy and gets you started within minutes to productively built ML solutions on your own machines. ML workspace is the ultimate tool for developers preloaded with a variety of popular data science libraries (Tensorflow, PyTorch, Keras, and MXnet) and dev tools (Jupyter, VS Code, and Tensorboard) perfectly configured, optimized, and integrated.
- Rmarkdown
- hctsa - series analysis using Matlab.
Python Frameworks and Tools
- Dash
- Python Package Index (PyPI)
- PyCharm
- Django - level Python Web framework that encourages rapid development and clean, pragmatic design.
- Flask
- Web2py - source web application framework written in Python allowing allows web developers to program dynamic web content. One web2py instance can run multiple web sites using different databases.
- Tornado - blocking network I/O, which can scale to tens of thousands of open connections.
- HTTPie
- Scrapy - 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.
- Sentry
- CherryPy - oriented HTTP web framework.
- Sanic
- Pyramid - world web application development and deployment more fun and more productive.
- TurboGears
- Falcon - performance Python web framework for building large-scale app backends and microservices with support for MongoDB, Pluggable Applications and autogenerated Admin.
- NumPy
- Pillow
- IPython
- GraphLab Create - scale, high-performance machine learning models.
- Pandas
- Matplotlib - quality figures in a variety of hardcopy formats and interactive environments across platforms.
- Scikit-Learn
- Ruby
- Ruby Documentation
- Ruby Community
- Ruby Gems
- Ruby courses by Coursera
- Learn Ruby course by Codecademy
- Ruby Glossary
- Ruby in Twenty Minutes Quickstart
- Getting started with a Ruby on Rails application on CircleCI.
- The Ruby Style Guide
- RubyMine
- Rails - application framework that includes everything needed to create database-backed web applications according to the [Model-View-Controller (MVC)](https://en.wikipedia.org/wiki/Model-view-controller) pattern. Understanding the MVC pattern is key to understanding Rails. MVC divides your application into three layers: Model, View, and Controller, each with a specific responsibility.
- Prettier for Ruby
- Active Admin
- Spree - commerce platform for Rails 6 with a modern UX, optional PWA frontend, REST API, GraphQL, several official extensions and 3rd party integrations.
- Sidekiq
- Kaminari
- Brakeman
- fastlane
- Fluentd
- Pylance
- Pyright
- AWS Chalice
- Pipenv
- Python Fire
- Bottle - framework for Python. It is distributed as a single file module and has no dependencies other than the [Python Standard Library](https://docs.python.org/library/).
- Neural Network Intelligence(NNI)
- Luigi - in.
- Locust
- spaCy
- PuLP
- Airbnb's Ruby Style Guide
- rbenv
- Capistrano
- React-Rails
- Pry
- dotenv
- Scientist
- Python Tools for Visual Studio(PTVS)
Python Learning Resources
- Python - level programming language. Python is used heavily in the fields of Data Science and Machine Learning.
- Python Developer’s Guide
- Azure Functions Python developer guide - us/azure/azure-functions/functions-reference).
- CheckiO
- Python Institute
- PCEP – Certified Entry-Level Python Programmer certification
- PCAP – Certified Associate in Python Programming certification
- Google's Python Education Class
- MTA: Introduction to Programming Using Python Certification
- Getting Started with Python in Visual Studio Code
- Google's Python Style Guide
- Real Python
- Intro to Python for Data Science
- Intro to Python by W3schools
- Codecademy's Python 3 course
- Learn Python with Online Courses and Classes from edX
- Python Courses Online from Coursera
- The Python Open Source Computer Science Degree by Forrest Knight
- PCPP – Certified Professional in Python Programming 2
Java Learning Resources

Programming Languages

Python 11 Ruby 5 Kotlin 3 MATLAB 3 Java 3 HTML 2 C# 1 JavaScript 1 Shell 1 Jupyter Notebook 1

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Bioinformatics-Guide

Tools

MATLAB Learning Resources

MATLAB Tools

Python Frameworks and Tools

Python Learning Resources

Java Learning Resources