Several software packages automatically generate up-to-date documentation from a markup language in the source code and elsewhere. These tools transform your code and markup into formats such as Unix manual (‘man’) page, Hypertext Markup Language (HTML) and Portable Document Format (PDF).
Provides an environnement for producing TeX documents. TeX Live gathers free TeX-related programs, macro packages and fonts to run a comprehensive system. It intends to include the main program and provide a support for many languages.
Generates documentation from source code. Doxygen is the de facto standard tool for generating documentation from annotated C++ sources, but it also supports other popular programming languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba, Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D. Doxygen can help users in three ways: (i) it can generate an on-line documentation browser (in HTML) and/or an off-line reference manual (in LaTeX) from a set of documented source files; (ii) users can configure Doxygen to extract the code structure from undocumented source files; (iii) users can also use doxygen for creating normal documentation.
Generates HTML pages of API (Application Programming Interface) documentation from Java source files. The Javadoc tool parses the declarations and documentation comments in a set of Java source files and produces a corresponding set of HTML pages describing (by default) the public and protected classes, nested classes (but not anonymous inner classes), interfaces, constructors, methods, and fields. The users can use it to generate the API documentation or the implementation documentation for a set of source files. The Javadoc tool can be applied to entire packages, individual source files, or both.
Provides an easy way to build XML files following the Helmholtz Open BioInformatics Technology network (HOBIT) format descriptions from inside the user's own programs. BioDOM is designed to be a modular system which can easily be extended as necessary to accomodate new formats. Additionally, it provides functions to convert native non-XML output of various bioinformatic tools to the HOBIT XML formats. In addition to these functions, there are conversion functions for many commonly used non-XML formats, which allow traditional tools and services a smooth transition from their data formats towards the XML formats.
A Doxygen-like documentation system for R. Roxygen allows in-source specification of Rd files, collation and namespace directives. The goal of Roxygen is to make documenting user’s code as easy as possible. Roxygen provides a number of advantages over writing Rd files by hand: (i) code and documentation are adjacent; (ii) Roxygen dynamically inspects the objects; (iii) it abstracts over the differences in documenting methods, generics and classes.
Assesses integrity and quality of clinical and lab data within a clinical trial. Rave Trial Assurance is an application allowing the analysis of data related to a specific trial to determine which trends may impact its integrity or quality. This program also enables contextual comparison of lab and clinical data and includes features for generating reports and presentation of results.
Detects and escapes a wide variety of problematic text strings so that they are not erroneously converted into other representations upon importation into Excel. Microsoft Excel automatically converts certain gene symbols, database accessions, and other alphanumeric text and numbers into dates, scientific notation, and other numerical representations, which may lead to subsequent, irreversible corruption of the imported text.