Bioinformatics-Guide

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

Last synced: about 3 hours ago
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Tools
- Retrofit - safe HTTP client for Android and Java develped by Square.
- Guava
- 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.
- IntelliJ IDEA
- 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.
- YourKit
- PhpStorm
- Composer
- CodeIgniter
- Laravel
- Symfony
- Slim
- 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.
- 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.
- GraalVM - based languages like Java, Scala, Clojure, Kotlin, and LLVM-based languages such as C and C++.
- 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.
- 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 Flink - and batch-processing capabilities with elegant and fluent APIs in Java and Scala.
- 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.
- 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).
- Java SE
- JDK Development Tools
- 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.
- 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.
- JaCoCo
- Junit
- Mockito
- SpotBugs
- 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.
- 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
- PHP Intelephense
- PHP Tools for Visual Studio/VS Code
- DesignPatternsPHP
- 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.
- Swoole - driven asynchronous & coroutine-based concurrency networking communication engine with high performance written in C and C++ for PHP.
- Java Design Patterns
- Guzzle
- okhttp
- LeakCanary
- Elasticsearch
- PHPUnit - oriented testing framework for PHP. It is an instance of the xUnit architecture for unit testing frameworks.
- 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.
- Whoops - of-the-box, it provides a pretty error interface that helps you debug your web projects, but at heart it's a simple yet powerful stacked error handling system.
Python Frameworks and Tools
- PyCharm
- RubyMine
- Matplotlib - quality figures in a variety of hardcopy formats and interactive environments across platforms.
- Python Package Index (PyPI)
- Django - level Python Web framework that encourages rapid development and clean, pragmatic design.
- Prettier for Ruby
- 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.
- 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.
- Falcon - performance Python web framework for building large-scale app backends and microservices with support for MongoDB, Pluggable Applications and autogenerated Admin.
- Pillow
- IPython
- Pandas
- Scikit-Learn
- Ruby
- Ruby Documentation
- Ruby Community
- Ruby Gems
- Ruby courses by Coursera
- Learn Ruby course by Codecademy
- Ruby in Twenty Minutes Quickstart
- 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
- Brakeman
- fastlane
- Fluentd
- Python Tools for Visual Studio(PTVS)
- Airbnb's Ruby Style Guide
- Python Fire
- Scientist
- Capistrano
- dotenv
- Luigi - in.
- Locust
- Pry
- rbenv
- React-Rails
- Pipenv
- spaCy
- AWS Chalice
- Neural Network Intelligence(NNI)
- 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/).
- Pylance
- Pyright
- PuLP
- Python Tools for Visual Studio(PTVS)
- HTTPie
- Getting started with a Ruby on Rails application on CircleCI.
- Sanic
MATLAB Tools
- Rmarkdown
- An Introduction to R
- CatBoost
- 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.
- YALMIP
- 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
- 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.
- LightGBM
- MLR
- 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
- hctsa - series analysis using Matlab.
- 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.
- 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
- 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.
Java Learning Resources
MATLAB Learning Resources
Python Learning Resources

Programming Languages

Python 12 Ruby 5 MATLAB 3 Kotlin 3 Java 3 PHP 2 HTML 2 Jupyter Notebook 1 JavaScript 1 Shell 1

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Tools

Indexes

Applications

Experiments

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Bioinformatics-Guide

Tools

Python Frameworks and Tools

MATLAB Tools

Java Learning Resources

MATLAB Learning Resources

Python Learning Resources