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knitr is a software engine for dynamic report generation with R. [1] [2] It is a package in the programming language R that enables integration of R code into LaTeX, LyX, HTML, Markdown, AsciiDoc, and reStructuredText documents. The purpose of knitr is to allow reproducible research in R through the means of literate programming.
R is a programming language for statistical computing and data visualization. It has been adopted in the fields of data mining, bioinformatics and data analysis. [9] The core R language is augmented by a large number of extension packages, containing reusable code, documentation, and sample data. R software is open-source and free software.
DOT is a graph description language, developed as a part of the Graphviz project. DOT graphs are typically stored as files with the .gv or .dot filename extension — .gv is preferred, to avoid confusion with the .dot extension used by versions of Microsoft Word before 2007.
MATLAB (an abbreviation of "MATrix LABoratory" [18]) is a proprietary multi-paradigm programming language and numeric computing environment developed by MathWorks.MATLAB allows matrix manipulations, plotting of functions and data, implementation of algorithms, creation of user interfaces, and interfacing with programs written in other languages.
Markdown [9] is a lightweight markup language for creating formatted text using a plain-text editor. John Gruber created Markdown in 2004 as an easy-to-read markup language. [9] Markdown is widely used for blogging and instant messaging, and also used elsewhere in online forums, collaborative software, documentation pages, and readme files.
Examples of domain-specific programming languages include HTML, Logo for pencil-like drawing, Verilog and VHDL hardware description languages, MATLAB and GNU Octave for matrix programming, Mathematica, Maple and Maxima for symbolic mathematics, Specification and Description Language for reactive and distributed systems, spreadsheet formulas and ...
A mathematical markup language is a computer notation for representing mathematical formulae, based on mathematical notation.Specialized markup languages are necessary because computers normally deal with linear text and more limited character sets (although increasing support for Unicode is obsoleting very simple uses).
By minimizing these systematic variations, true biological differences can be found. To determine whether normalization is needed, one can plot Cy5 (R) intensities against Cy3 (G) intensities and see whether the slope of the line is around 1. An improved method, which is basically a scaled, 45 degree rotation of the R vs. G plot is an MA-plot. [4]