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Rhea (pipeline)
Rhea is a bioinformatic pipeline written in R (programming language), 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 Multidimensional scaling#Types, 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 (programming language), 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 (mytholo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
R (programming Language)
R is a programming language for statistical computing and graphics supported by the R Core Team and the R Foundation for Statistical Computing. Created by statisticians Ross Ihaka and Robert Gentleman, R is used among data miners, bioinformaticians and statisticians for data analysis and developing statistical software. Users have created packages to augment the functions of the R language. According to user surveys and studies of scholarly literature databases, R is one of the most commonly used programming languages used in data mining. R ranks 12th in the TIOBE index, a measure of programming language popularity, in which the language peaked in 8th place in August 2020. The official R software environment is an open-source free software environment within the GNU package, available under the GNU General Public License. It is written primarily in C, Fortran, and R itself (partially self-hosting). Precompiled executables are provided for various operating systems. R ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GitHub
GitHub, Inc. () is an Internet hosting service for software development and version control using Git. It provides the distributed version control of Git plus access control, bug tracking, software feature requests, task management, continuous integration, and wikis for every project. Headquartered in California, it has been a subsidiary of Microsoft since 2018. It is commonly used to host open source software development projects. As of June 2022, GitHub reported having over 83 million developers and more than 200 million repositories, including at least 28 million public repositories. It is the largest source code host . History GitHub.com Development of the GitHub.com platform began on October 19, 2007. The site was launched in April 2008 by Tom Preston-Werner, Chris Wanstrath, P. J. Hyett and Scott Chacon after it had been made available for a few months prior as a beta release. GitHub has an annual keynote called GitHub Universe. Organizational ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Free R (programming Language) Software
Free may refer to: Concept * Freedom, having the ability to do something, without having to obey anyone/anything * Freethought, a position that beliefs should be formed only on the basis of logic, reason, and empiricism * Emancipate, to procure political rights, as for a disenfranchised group * Free will, control exercised by rational agents over their actions and decisions * Free of charge, also known as gratis. See Gratis vs libre. Computing * Free (programming), a function that releases dynamically allocated memory for reuse * Free format, a file format which can be used without restrictions * Free software, software usable and distributable with few restrictions and no payment * Freeware, a broader class of software available at no cost Mathematics * Free object ** Free abelian group ** Free algebra ** Free group ** Free module ** Free semigroup * Free variable People * Free (surname) * Free (rapper) (born 1968), or Free Marie, American rapper and media personality ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rhea (mythology)
Rhea or Rheia (; Ancient Greek: Ῥέα or Ῥεία ) is a mother goddess in ancient Greek religion and Greek mythology, the Titaness daughter of the earth goddess Gaia and the sky god Uranus, himself a son of Gaia. She is the older sister of Cronus, who was also her consort, and the mother of the five eldest Olympian gods Hestia, Demeter, Hera, Poseidon and Zeus, and the king of the Underworld, Hades. When Cronus learnt that he was destined to be overthrown by one of his children like his father was before him, he swallowed all the children Rhea bore as soon as they were born. When Rhea had her sixth and final child, Zeus, she spirited him away and hid him in Crete, giving Cronus a rock to swallow instead, thus saving her youngest son who would go on to challenge his father's rule and rescue the rest of his siblings. Following Zeus' defeat of Cronus and the rise of the Olympian gods into power, Rhea withdraws her role as the queen of the gods to become a supporting figure ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Multidimensional Scaling
Multidimensional scaling (MDS) is a means of visualizing the level of similarity of individual cases of a dataset. MDS is used to translate "information about the pairwise 'distances' among a set of n objects or individuals" into a configuration of n points mapped into an abstract Cartesian space. More technically, MDS refers to a set of related ordination techniques used in information visualization, in particular to display the information contained in a distance matrix. It is a form of non-linear dimensionality reduction. Given a distance matrix with the distances between each pair of objects in a set, and a chosen number of dimensions, ''N'', an MDS algorithm places each object into ''N''-dimensional space (a lower-dimensional representation) such that the between-object distances are preserved as well as possible. For ''N'' = 1, 2, and 3, the resulting points can be visualized on a scatter plot. Core theoretical contributions to MDS were made by James O. Ramsay of M ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beta Diversity
Beta (, ; uppercase , lowercase , or cursive ; grc, βῆτα, bē̂ta or ell, βήτα, víta) is the second letter of the Greek alphabet. In the system of Greek numerals, it has a value of 2. In Modern Greek, it represents the voiced labiodental fricative while in borrowed words is instead commonly transcribed as μπ. Letters that arose from beta include the Roman letter and the Cyrillic letters and . Name Like the names of most other Greek letters, the name of beta was adopted from the acrophonic name of the corresponding letter in Phoenician, which was the common Semitic word ''*bait'' ('house'). In Greek, the name was ''bêta'', pronounced in Ancient Greek. It is spelled βήτα in modern monotonic orthography and pronounced . History The letter beta was derived from the Phoenician letter beth . Uses Algebraic numerals In the system of Greek numerals, beta has a value of 2. Such use is denoted by a number mark: Β′. Computing Finance Beta is used i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Alpha Diversity
In ecology, alpha diversity (α-diversity) is the mean species diversity in a site at a local scale. The term was introduced by R. H. WhittakerWhittaker, R. H. (1960) Vegetation of the Siskiyou Mountains, Oregon and California. Ecological Monographs, 30, 279–338. Whittaker, R. H. (1972). Evolution and Measurement of Species Diversity. Taxon, 21, 213-251. together with the terms beta diversity (β-diversity) and gamma diversity (γ-diversity). Whittaker's idea was that the total species diversity in a landscape (gamma diversity) is determined by two different things, the mean species diversity in sites at a more local scale (alpha diversity) and the differentiation among those sites (beta diversity). Scale considerations Both the area or landscape of interest and the sites within it may be of very different sizes in different situations, and no consensus has been reached on what spatial scales are appropriate to quantify alpha diversity. It has therefore been proposed that the de ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Operational Taxonomic Unit
An Operational Taxonomic Unit (OTU) is an operational definition used to classify groups of closely related individuals. The term was originally introduced in 1963 by Robert R. Sokal and Peter H. A. Sneath in the context of numerical taxonomy, where an "Operational Taxonomic Unit" is simply the group of organisms currently being studied. In this sense, an OTU is a pragmatic definition to group individuals by similarity, equivalent to but not necessarily in line with classical Linnaean taxonomy or modern evolutionary taxonomy. Nowadays, however, the term "OTU" is commonly used in a different context and refers to clusters of (uncultivated or unknown) organisms, grouped by DNA sequence similarity of a specific taxonomic marker gene (originally coined as mOTU; molecular OTU). In other words, OTUs are pragmatic proxies for "species" (microbial or metazoan) at different taxonomic levels, in the absence of traditional systems of biological classification as are available for macroscopi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatic Pipeline
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for ''in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (esp. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Windows
Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for servers, and Windows IoT for embedded systems. Defunct Windows families include Windows 9x, Windows Mobile, and Windows Phone. The first version of Windows was released on November 20, 1985, as a graphical operating system shell for MS-DOS in response to the growing interest in graphical user interfaces (GUIs). Windows is the most popular desktop operating system in the world, with 75% market share , according to StatCounter. However, Windows is not the most used operating system when including both mobile and desktop OSes, due to Android's massive growth. , the most recent version of Windows is Windows 11 for consumer PCs and tablets, Windows 11 Enterprise for corporations, and Windows Server 2022 for servers. Genealogy By marketing ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MIT License
The MIT License is a permissive free software license originating at the Massachusetts Institute of Technology (MIT) in the late 1980s. As a permissive license, it puts only very limited restriction on reuse and has, therefore, high license compatibility. Unlike copyleft software licenses, the MIT License also permits reuse within proprietary software, provided that all copies of the software or its substantial portions include a copy of the terms of the MIT License and also a copyright notice. , the MIT License was the most popular software license found in one analysis, continuing from reports in 2015 that the MIT License was the most popular software license on GitHub. Notable projects that use the MIT License include the X Window System, Ruby on Rails, Nim, Node.js, Lua, and jQuery. Notable companies using the MIT License include Microsoft ( .NET), Google ( Angular), and Meta (React). License terms The MIT License has the identifier MIT in the SPDX License List. It is ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OpenSUSE
openSUSE () is a free and open-source software, free and open source RPM Package Manager, RPM-based Linux distribution developed by the openSUSE project. The initial release of the community project was a beta version of SUSE Linux 10.0. Additionally the project creates a variety of tools, such as YaST, Open Build Service, openQA, Snapper, Machinery, Portus, KIWI (openSUSE), KIWI and OSEM. Product history In the past, the SUSE Linux company had focused on releasing the SUSE Linux Personal and SUSE Linux Professional box sets which included extensive printed documentation that was available for sale in retail stores. The company's ability to sell an open source product was largely due to the closed-source development process used. Although SUSE Linux had always been free software product licensed with the GNU General Public License (GNU GPL), it was only freely possible to retrieve the source code of the next release 2 months after it was ready for purchase. SUSE Linux' strate ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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