Search Results for "java expression evaluator" - Page 2

Chromatin accessibility plays a key role in epigenetic regulation of gene activation and silencing. Open chromatin regions allow regulatory elements such as transcription factors and polymerases to bind for gene expression while closed chromatin regions prevent the activity of transcriptional machinery. Recently, nucleosome occupancy and methylome sequencing (NOMe-seq) has been developed for simultaneously profiling of chromatin accessibility and DNA methylation on single molecules. However,...

An EDM calibration baseline is used to derive specific instrument errors of the electronic distance measurement (EDM) unit of a total station. EDMFit is a simple adjustment tool to estimate the EDM calibration parameters (addition constant and/or scale parameter). The adjustment process is according to ISO 17123-4. The parameters are checked for significance, to avoid an overestimation. Based on two classical hypothesis testing, EDMFit provides a reliable outlier detection. For...

This is a parser in Java for Lisp S-expressions. An S-expression or sexp (for symbolic expression) is a convention for representing data using parentheses.

A Tool for Retrieval, Visualization and Analysis of biological Pathways. Import a Gene or Protein Set from any Excel file. Automatically find signaling Pathways from KEGG. Integrate your Data in Seconds with a live interactive Force-directed Layout.

Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional...

expressionCalc is a Mathematical expression solver. It has a Java implementation (for cross platform) and a C# implementation (for Windows). Support most of the Mathematical functions including log, sin, a sin etc. Implemented based on the expression solving technique of BODMAS.

ExpressionOasis is a java based framework for evaluating the various type of expressions like arithmatic, logic expression etc. The framework is flexible enough to define any new grammer rules or operators.

This package contains code for use with Short Read DNA Sequencing technologies, and includes packages for ChIP-Seq, Whole Transcriptome Shotgun Sequencing, Whole Genome Shotgun Sequencing, SNP Detection, Transcript expression and file conversion.

The characterization of genomic sites is a major challenge in the understanding and exploitation of next generation sequencing data. Most genomic sites are represented by short, degenerated motifs with a scattered distribution and sometimes with biological function (ex: regulation of gene expression, splicing patterns or epigenetics signals). These motifs are associated with a huge amount of noise and thus, the development of a computational platform for accurate detection of genomic sites...

This project gives a mathematical parser for converting a simple string expression into a result which can be managed for using in other calculations, all in Java. Using a couple lines of code, you'll be able to parse complex arithmetic expressions efficiently. This library is powered by Dijkstra's Shuting-yard algorithm. The library has no dependencies with other external libraries. Dependency <dependency> <groupId>com.google.code.mathparser-java</groupId> <artifactId>mathparser-java</artifactId> <version>1.0.0</version> </dependency> Expressions supported (Mar/09/2013) - Arithmetic operations. ...

This plugin allow to visualize several e.g. gene expression values simultanously using pie charts. * Please cite http://www.biomedcentral.com/1752-0509/4/164 *

This project provides an interface to Java expression evaluator software. It does not itself provide expression capabilities but instead provides a common interface.

FastMap is Java based software that performs quantitative trait locus mapping for gene expression data (eQTL Mapping).

Java library for parsing and evaluating math expressions. Javadoc is available at http://bracer.sourceforge.net/javadoc/ P.S. This library depends on Apache Commons Math, so don't forget to include commons-math-2.2.jar to your project.

Plotting of mathematical functions, including math expression evaluation

Jep is a Java package for parsing and evaluating mathematical expressions. It currently supports user defined variables, constants, and functions. The open-source Jep project was halted in favor of commercial development of version 3.0 upwards.

The Katsura tool overlays microarray gene expression data, proteomics, and similar biological data onto metabolic pathways. [Pathogen Functional Genomics Resource Center (PFGRC) @ J. Craig Venter Institute (JCVI)]

Microarray Gene Expression Database Group and OMG Gene Expression Standard (MAGE)

JFlux is a java library and graphical user interface to work with flow cytometry data. In particular, it is adapted to the COPAS biosorter and can analyze expression profiles.

SAFEGUI is a graphical interface to the safe R package which performs resampling based categorical significance testing for gene expression data.

Genevar (GENe Expression VARiation) is a platform of database and web services for the integrative analysis and visulization of SNP-gene assocaitaions in eQTL studies.

GEM is a computational method for identification of transcription factor modulators, using expression datasets. The method tests if the correlation between factor and target gene depends on the expression of the modulator.

DragMath is a drag and drop equation editor in the form of a Java applet. Once an expression is created the user can convert it into a variety of different linear syntax for mathematics, including MathML, LaTeX, Maple, Maxima or any user defined style. PLEASE NOTE: active code development has moved to GitHub. https://github.com/maths/dragmath

SLEDRIDE: Simplified Learning about Expression Data Running in a Desktop Environment. To provide a general workbench for pipe-lining microarray gene expression data from supervised learning results into unsupervised learning methods.

A project to help students calculate symbolic derivatives and integrals. Plus, a Java expression tree library for developers who may need to do such things in their programs. The project has moved to github: https://github.com/generalpenguin89/calchelper