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Rhea

Rhea is a bioinformatic pipeline written in R language for the analysis of microbial profiles. It was released during the end of 2016 and it is publicly available through a GitHub repository.
Starting with an Operational taxonomic unit (OTU) table, the pipeline contains scripts that perform the following common analytical steps:
# Normalization of the OTU table
# Calculation of the alpha diversity for each sample
# Calculation of beta diversity and visualization of the results with PCoA
# Taxonomic binning
# Statistical testing
# Correlation analysis
The name Rhea was primarily given to the pipeline as a phonetic and visual link to the R language used throughout development. Moreover, as stated in the original publication, the name was chosen to reflect the flowing and evolving nature of the scripts, as "flow" is one of the suggested etymology of the name of the mythological goddess Rhea.
Developed by Ilias Lagkouvardos, Sandra Fischer, Neeraj Kumar, Thomas Clavel

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  • dwm by suckless.org

    dwm is a dynamic, minimalist tiling window manager for the X Window System that has influenced the development of several other X window managers, including xmonad and awesome. It is externally...

    Latest version of dwm is 6.1 and it was released on 2015-11-09.

    Tags: Application Launchers, Free Software Programmed In C, Free X Window Managers, Software Using The Mit License, Tiling Window Managers, Unix Windowing Systemrelated Software
  • Open Cobalt by Community source and Duke University

    Open Cobalt is a free and open-source software platform for constructing, accessing, and sharing virtual worlds both on local area networks or across the Internet, without any requirement for...

    Tags: 3d Scenegraph Apis, Alpha Software, Crossplatform Free Software, Free Simulation Software, Free Software Projects, Groupware, Information Technology Management, Integrated Development Environments, Free Software Distributions, Software Using The Mit License, User Interface Builders, Virtual Reality, Virtual Reality Communities
  • cURL

    cURL (/kɝl/ or /kə:l/) is a computer software project providing a library and command-line tool for transferring data using various protocols. The cURL project produces two products, libcurl and...

    Tags: 1997 Software, C Libraries, Commandline Software, Crossplatform Free Software, Download Managers, Free Ftp Clients, Free Software Programmed In C, Free Web Crawlers, Hypertext Transfer Protocol Clients, Software Using The Mit License, Web Scraping
  • OpenEmbedded by 75+ developers

    OpenEmbedded is a software framework used for creating Linux distributions aimed for, but not restricted to, embedded devices. The build system is based on BitBake recipes, which behave like Gentoo...

    Tags: Embedded Linux, Build Automation, Personal Digital Assistant Software, Software Using The Mit License
  • ncdu by Yoran Heling

    ncdu (NCurses Disk Usage) is a disk utility for Unix systems. Its name refers to its similar purpose to the du utility, but ncdu uses a TUI under the curses programming library.]Users can navigate...

    Latest version of ncdu is 1.12 and it was released on 2016-08-24.

    Tags: Disk Usage Analysis Software, Software Using The Mit License, Free Software Programmed In C, 2007 Software, Curses, Unix File Systemrelated Software, Software That Uses Ncurses
  • Capybara by Thomas Walpole

    Capybara is a web-based test automation software that simulates scenarios for user stories and automates web application testing for behavior-driven software development. It is a part of the...

    Tags: Software Testing Tools, Software Using The Mit License, Graphical User Interface Testing, Load Testing Tools, Unit Testing Frameworks, Web Development Software, Web Scraping
  • Prosody by Prosody dev team

    Prosody (formerly lxmppd) is a cross-platform XMPP server written in Lua. Its development goals include low resource usage, ease of use, and...

    Latest version of Prosody is 0.9.12 and it was released on 2017-01-10.

    Tags: Instant Messaging Server Software, Free Software Programmed In Lua, Software Using The Mit License
  • CLiki

    CLiki is an open source wiki application written in Common Lisp, that was under development from 2002 to 2005. CLiki was first presented at the International Lisp Conference 2002. CLiki was the...

    Latest version of CLiki is 0.4.4 and it was released on 2005-05-28.

    Tags: Free Wiki Software, Common Lisp Software, Software Using The Mit License
  • CERN httpd by CERN / World Wide Web Consortium

    CERN httpd (later also known as ]] (url=HTTP)]] originally developed at CERN from 1990 onwards by Tim Berners-Lee, Ari Luotonen and Henrik Frystyk Nielsen. Implemented in C, it was the first ever...

    Latest version of CERN httpd is 3.0A and it was released on 1996-07-15.

    Tags: Free Web Server Software, Discontinued Software, History Of The Internet, Software Using The Mit License, Publicdomain Software With Source Code
  • AidaWeb by Janko Mivšek and

    Aida/Web is an object-oriented, open source Smalltalk web application server using the model-view-controller (MVC) architectural...

    Latest version of Aida/Web is 6.7 and it was released on 2014-09-14.

    Tags: Web Frameworks, Free Software Application Servers, Smalltalk Programming Language Family, Software Using The Mit License
  • OpenEpi by AG Dean, KM Sullivan, MM Soe

    OpenEpi is a free, web-based, open source, operating system-independent series of programs for use in epidemiology, biostatistics, public health, and medicine, providing a number of epidemiologic...

    Latest version of OpenEpi is 3.03 and it was released on 2014-09-22.

    Tags: Biostatistics, Epidemiology, Free Statistical Software, Software Using The Mit License
  • EAS3

    EAS3 (EAS = Ein-Ausgabe-System) is a software toolkit for reading and writing structured binary data with geometry information and for postprocessing of these data. It is meant to exchange...

    Latest version of EAS3 is 1.6.7 and it was released on 2009-04-14.

    Tags: Free Science Software, Free Software Programmed In C, Free Software Programmed In Fortran, Computer File Formats, Software Using The Mit License
  • fdupes by Adrián López

    fdupes is a program written by Adrián López to scan directories for duplicate files, with options to list, delete or replace the files with hardlinks pointing to the duplicate. It first compares...

    Tags: Unix File Systemrelated Software, Software Using The Mit License
  • x2x

    x2x allows the console (keyboard and mouse) on one X terminal to be used to control another X terminal. It also provides ancillary functions like clipboard sharing. x2x is an international trademark...

    Latest version of x2x is 1.27 and it was released on 2003-02-01.

    Tags: X Window Managers, Crossplatform Software, 1996 Software, Free Networkrelated Software, Free Software Programmed In C, Software Using The Mit License, Remote Desktop Software For Linux
  • Twisted by Community

    Twisted is an event-driven network programming framework written in Python and licensed under the MIT License. Twisted projects variously support TCP, UDP, SSL/TLS, IP multicast, Unix domain...

    Tags: Free Networkrelated Software, Free Software Programmed In Python, Free System Software, Python Libraries, Python Software, Software Using The Mit License
  • Spyder

    Spyder (formerly Pydee) is an open source cross-platform integrated development environment (IDE) for scientific programming in the Python language. Spyder integrates NumPy, SciPy, Matplotlib and...

    Latest version of Spyder is 3.2.3 and it was released on 2017-09-11.

    Tags: Free Integrated Development Environments, Free Integrated Development Environments For Python, Python Development Tools, Free Mathematics Software, Free Science Software, Python Software, Software Using The Mit License
  • Pinta by {{Plain list | * Cameron White * Robert Nordan * Olivier Dufour }}

    Pinta is an open-source, cross-platform bitmap image drawing and editing program inspired by Paint.NET, a similar image editing program which is limited to Microsoft Windows. Pinta has more features...

    Latest version of Pinta is 1.6 and it was released on 2015-03-01.

    Tags: 2010 Software, Crossplatform Free Software, Free Graphics Software, Free Raster Graphics Editors, Free Software Programmed In C Sharp, Gnome Applications, Graphics Software That Uses Gtk, Raster Graphics Editors For Linux, Raster Graphics Editors, Software That Uses Mono, Software Using The Mit License
  • LifeLines by Larry Hamilton and the LifeLines Team

    LifeLines is a free open-source genealogy software tool to assist family history research. LifeLines primary strengths are its powerful scripting language and the ability to easily import and export...

    Latest version of LifeLines is 3.1.1 and it was released on 2016-03-17.

    Tags: Free Genealogy Software, Free Software Programmed In C, Software Using The Mit License
  • Diskspd by Microsoft Corporation

    Diskspd is a commandline tool for storage benchmarking on Microsoft Windows that generates a variety of requests against computer files, partitions or storage devices and presents collected...

    Latest version of Diskspd is 2.0.17 and it was released on 2016-05-07.

    Tags: Computer Benchmarks, Storage Software, Utilities For Windows, Software Using The Mit License
  • MapServer by Stephen Lime

    MapServer is an open source development environment for building spatially enabled internet applications. It can run as a CGI program or via MapScript which supports several programming languages...

    Latest version of MapServer is 7.0.6 and it was released on 2017-06-21.

    Tags: Free Gis Software, University Of Minnesota Software, Software Using The Mit License
  • Threejs by Three.js Authors

    Three.js is a cross-browser JavaScript library/API used to create and display animated 3D computer graphics in a web browser. Three.js uses WebGL. The source code is hosted in a repository on...

    Latest version of Three.js is r87 and it was released on 2017-08-18.

    Tags: 2010 Software, 3d Scenegraph Apis, Crossplatform Software, Free 3d Graphics Software, Graphics Libraries, Javascript Libraries, Software Using The Mit License, Webgl
  • ObjectOriented Graphics Rendering Engine by The OGRE Team

    Object-Oriented Graphics Rendering Engine (OGRE) is a scene-oriented, real-time, 3D rendering engine, as opposed to a game engine. OGRE is cross-platform and abstracts from the underlying system...

    Latest version of Object-Oriented Graphics Rendering Engine is 1.10.7 (Xalafu) and it was released on 2017-07-30.

    Tags: 2005 Software, 3d Scenegraph Apis, Application Programming Interfaces, C Libraries, Crossplatform Software, Free 3d Graphics Software, Free Game Engines, Free Software Programmed In C, Game Engines For Linux, Graphics Libraries, Software Using The Mit License, Video Game Development Software
  • AFrame by A-Frame Authors

    A-Frame is an open-source web framework for building virtual reality (VR) experiences. It is primarily maintained by Mozilla and the WebVR community. It is an entity component system framework for...

    Latest version of A-Frame is 0.6.1 and it was released on 2017-07-19.

    Tags: 2015 Software, 3d Scenegraph Apis, Crossplatform Software, Free 3d Graphics Software, Javascript Web Frameworks, Rich Internet Application Frameworks, Software Using The Mit License, Virtual Reality, Webgl
  • Little CMS by Marti Maria,Bob Friesenhahn,Kai-Uwe Behrmann,Stuart Nixon,Jordi Vilar,Richard Hughes,Auke Nauta,Chris Evans (Google),Lorenzo Ridolfi,Robin Watts (Artifex),Shawn Pedersen,Andrew Brygin,Samuli Suominen,Florian Höch,Aurelien Jarno,Claudiu Cebuc,Michael Vhrel (Artifex),Michal Cihar,Daniel Kaneider,Mateusz Jurczyk (Google),Paul Miller,Sébastien Léon,Christian Schmitz,XhmikosR,Stanislav Brabec (SuSe),Leonhard Gruenschloss (Google),Patrick Noffke,Christopher James Halse Rogers,John Hein

    Little CMS or LCMS is an open source color management system, released as a software library for use in other programs which will allow the use of International Color Consortium profiles. It is...

    Latest version of Little CMS is 2.8 and it was released on 2016-07-22.

    Tags: Graphics Libraries, Free Graphics Software, Software Using The Mit License
  • Dovecot by Timo Sirainen and contributors

    Dovecot is an open-source IMAP and POP3 server for Linux/UNIX-like systems, written primarily with security in mind. Timo Sirainen originated Dovecot and first released it in July 2002. Dovecot...

    Latest version of Dovecot is 2.2.31 and it was released on 2017-06-26.

    Tags: Free Email Server Software, Free Software Programmed In C, Email Server Software For Linux, Software Using The Mit License
  • XDM by X.Org Foundation

    XDM (in full, the X Display Manager) is the default display manager for the X Window System. It is a bare-bones X display manager. It was introduced with X11 Release 3 in October 1988, to support...

    Latest version of XDM is 1.1.11 and it was released on 2011-09-25.

    Tags: Free System Software, Software Using The Mit License, X Display Managers
  • Taskwarrior by Paul Beckingham, Federico Hernandez, David J Patrick, John Florian, Cory Donnelly, Johannes Schlatow, Dirk Deimeke, Scott Kostyshak, Renato Alves, Wim Schuermann, Tomas Babej

    Taskwarrior is an open-source, cross platform time and task management tool. It has a command-line interface rather than a graphical user interface. Taskwarrior uses concepts and techniques...

    Latest version of Taskwarrior is 2.5.1 and it was released on 2016-02-24.

    Tags: Administrative Software, Timetracking Software, Task Management Software, Free Task Management Software, Free Personal Information Managers, Crossplatform Free Software, Free Calendaring Software, Software Using The Mit License
  • Dropbear by Matt Johnston

    Dropbear is a software package written by Matt Johnston that provides a Secure Shell-compatible server and client. It is designed as a replacement for standard OpenSSH for environments with low...

    Tags: Cryptographic Software, Free Networkrelated Software, Free Security Software, Secure Shell, Software Using The Mit License
  • Network Audio System by Jon Trulson

    The Network Audio System (NAS) is an open-source, network-transparent, client-server audio transport system. NAS works on Unix and Microsoft Windows platforms. The project began in the early 1990s....

    Latest version of Network Audio System is 1.9.4 and it was released on October 7, 2013.

    Tags: Free Audio Software, Free Software Programmed In C, Software Using The Mit License
  • Roundup by Richard Jones, Roundup Initiative

    Roundup is an open-source issue or bug tracking system featuring a command-line, web and e-mail interface. It is written in Python and designed to be highly customizable.The primary user interface...

    Latest version of Roundup is 1.5.1 and it was released on 2016-01-11.

    Tags: Bug And Issue Tracking Software, Free Project Management Software, Free Software Programmed In Python, Software Using The Mit License, Web Applications, Python Software
  • Blosxom by Rael Dornfest

    Blosxom is a free-software weblog program (and simple content management system) written in Perl by Rael Dornfest. It uses the pre-existing file system instead of a database management system,...

    Tags: Free Content Management Systems, Blog Software, Free Software Programmed In Perl, Software Using The Mit License
  • Jekyll by Tom Preston-Werner, Nick Quaranto, Parker Moore

    Jekyll is a simple, blog-aware, static site generator for personal, project, or organization sites. Written in Ruby by Tom Preston-Werner, GitHub's co-founder, it is distributed under an open source...

    Tags: Free Static Website Generators, Blog Software, Free Software Programmed In Ruby, Software Using The Mit License
  • concrete5 by https://www.concrete5.org/

    concrete5 is an open-source content management system (CMS) for publishing content on the World Wide Web and intranets. Concrete5 was designed for ease of use, for users with a minimum of technical...

    Latest version of concrete5 is 8.1.0 and it was released on 2017-01-24.

    Tags: Free Content Management Systems, Free Software Programmed In Php, Blog Software, Software Using The Mit License
  • nouveau

    nouveau is a free and open-source graphics device driver for Nvidia video cards and the Tegra family of SoCs written by independent software engineers, with minor help from Nvidia employees. The...

    Latest version of nouveau is 1.0.15 and it was released on 2017-04-21,.

    Tags: 3d Graphics Software, Direct Rendering Infrastructure, Free Device Drivers, Free Software Programmed In C, Freedesktoporg, Linux Drivers, Nvidia Software, Software Using The Mit License
  • Coderity by Michael Houghton

    Coderity is a free and open-source content management system (CMS) based on PHP, CakePHP and MySQL. Coderity was released on January 20, 2015, by its founder, Michael Houghton. Coderity is released...

    Tags: 2015 Software, Blog Software, Content Management Systems, Free Content Management Systems, Free Software Programmed In Php, Website Management, Software Using The Mit License
  • Tao Classic

    The Tao Classic is a C# library giving .NET and Mono developers access to popular graphics and gaming libraries like OpenGL and SDL. Tao Classic is the direct continuation of the abandoned Tao...

    Latest version of Tao Classic is 3.0-alpha and it was released on 2013-01-27.

    Tags: 3d Graphics Software, Mono, Software Using The Mit License
  • Tao Framework

    The Tao Framework is a C# library giving .NET and Mono developers access to popular graphics and gaming libraries like OpenGL and SDL. It was originally developed by the C# OpenGL programmer Randy...

    Latest version of Tao Framework is 2.1 and it was released on 2008-05-01.

    Tags: 3d Graphics Software, Mono, Software Using The Mit License
  • openFrameworks by Zachary Lieberman,Theo Watson,Arturo Castro

    openFrameworks is an open source toolkit designed for "creative coding". OpenFrameworks is written in C++ and built on top of OpenGL. It runs on Microsoft Windows, macOS, Linux, iOS, Android and...

    Latest version of openFrameworks is [http://www.openframeworks.cc/download 0.9.8] and it was released on 2016-11-22.

    Tags: 3d Graphics Software, Application Programming Interfaces, Free Computer Libraries, Software Using The Mit License
  • Bouncy Castle by Legion of the Bouncy Castle Inc.

    Bouncy Castle is a collection of APIs used in cryptography. It includes APIs for both the Java and the C# programming languages. The APIs are supported by a registered Australian charitable...

    Tags: Cryptographic Software, Java Libraries, Software Using The Mit License, Transport Layer Security Implementation
  • I2P The Anonymous Network

    The Invisible Internet Project (I2P) is a garlic routing using overlay network and darknet that allows applications to send messages to each other pseudonymously and securely. Uses include anonymous...

    Latest version of I2P - The Anonymous Network is 0.9.31 and it was released on 2017-08-07.

    Tags: I2p, Anonymity Networks, Anonymous File Sharing Networks, Crossplatform Free Software, Crossplatform Software, Cryptographic Software, Cryptographic Protocols, Dark Web, Free Communication Software, Free Multilingual Software, Free Networkrelated Software, Free Routing Software, Free Software Programmed In Java, Free And Opensource Android Software, Internet Privacy Software, Peertopeer Computing, Privacy Software, 2003 Software, Software Using The Mit License
  • PuTTY by Simon Tatham

    PuTTY is a free and open-source terminal emulator, serial console and network file transfer application. It supports several network protocols, including SCP, SSH, Telnet, rlogin, and raw socket...

    Latest version of PuTTY is 0.70 and it was released on 2017-07-08.

    Tags: 1998 Software, Crossplatform Free Software, Cryptographic Software, Free Communication Software, Free Software Programmed In C, Free Terminal Emulators, Secure Shell, Sftp Clients, Software Using The Mit License, Symbian Software
  • Godot Engine by Community developed

    Godot is a 2D and 3D cross-platform open source MIT licensed game engine developed by its community and used internally by several companies in Latin America before being released to the public. The...

    Latest version of Godot Engine is 2.1.4 and it was released on 2017-08-27.

    Tags: 2014 Software, Crossplatform Software, Free 3d Graphics Software, Free Software Programmed In C, Game Engines For Linux, Iphone Video Game Engines, Macos Programming Tools, Software Using The Mit License, Video Game Engines, Video Game Ide
  • Papervision3D

    Papervision3D is an open source, 3D graphics engine for rendering 3D content within Adobe Flash Player and Adobe AIR. Unlike modern Flash 3D engines such as Away3D and Flare3D, Papervision3D is not...

    Latest version of Papervision3D is 2.1.932 and it was released on {{Start date and age|2009|12}}.

    Tags: 3d Scenegraph Apis, Free 3d Graphics Software, Free Game Engines, Software Using The Mit License
  • PlayCanvas by Will Eastcott, Dave Evans, Vaios Kalpias-Illias, Kevin Rooney, Maksims Mihejevs

    PlayCanvas is an open source 3D game engine/interactive 3D application engine alongside a proprietary cloud-hosted creation platform that allows for simultaneous editing from multiple computers via...

    Tags: Cloud Applications, Collaborative Realtime Editors, Crossplatform Free Software, Free 3d Graphics Software, Free Game Engines, Free Software Programmed In Javascript, Graphics Libraries, Iphone Video Game Engines, Software Using The Mit License, Video Game Development Software, Video Game Engines, Web Applications, Web Development, Web Development Software, Web Software, Webgl
  • Seamless3d by Graham Perrett (AKA thyme)

    Seamless3d is an open source 3D modeling software available under the MIT license. The models for the virtual reality world Techuelife Island were created using Seamless3d technology. Techuelife...

    Latest version of Seamless3d is 3.004 and it was released on 2017-01-25.

    Tags: Free 3d Graphics Software, 3d Animation Software, Video Game Development Software, Windowsonly Free Software, Software Using The Mit License
  • GDAL by Open Source Geospatial Foundation

    The Geospatial Data Abstraction Library (GDAL) is a computer software library for reading and writing raster and vector geospatial data formats, and is released under the permissive X/MIT style free...

    Latest version of GDAL is 2.2.1 and it was released on 2017-06-23.

    Tags: C Libraries, Crossplatform Software, Data Structures Libraries And Frameworks, Free Computer Libraries, Free Gis Software, Gis File Formats, Software Using The Mit License
  • XeTeX

    XeTeX ( or ; see also Pronouncing and writing "TeX") is a TeX typesetting engine using Unicode and supporting modern font technologies such as OpenType, Graphite and Apple Advanced Typography (AAT)....

    Latest version of XeTeX is 0.99997 and it was released on 2017-03-16.

    Tags: 2007 Software, Digital Typography, Free Pdf Software, Free Tex Software, Linux Tex Software, Software Using The Mit License, Tex, Unicode
  • Banshee by Novell Inc.

    Banshee is a cross-platform open-source media player, called Sonance until 2005. Built upon Mono and Gtk#, it uses the GStreamer multimedia platform for encoding and decoding various media formats,...

    Tags: 2005 Software, Applications Using Dbus, Audio Player Software That Uses Gtk, Free Audio Software, Free Media Players, Free Software Programmed In C Sharp, Ipod Software, Jukeboxstyle Media Players, Linux Media Players, Macos Multimedia Software, Software That Uses Gstreamer, Software That Uses Mono, Software Using The Mit License, Windows Multimedia Software