Search Results for "bio-bwa" - Page 3

Combines the Tophat and Cuffdiff functions in one GUI interface. tophat and cuffdiff are required to be pre-installed in the system. By modifying the program, it can be used to execute any command line programs even R packages since R can also be run from commandlines. New functions: Batch processing function for Tophat. You can now execute as many mapping jobs as you want with tophat. This program will save the output into separate folders. An alert email will be sent to your email...

ViNSS View is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. ViNSS View allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, ViNSS View allows you to incorporate non-canonical base pairs into your drawing.

DeNovoCheck is intended to be used for inheritance analysis in NGS tio data. For rare dominant Mendelian diseases, patient-parent trios are often used to reduce the number of candidate variants. The algorithm bases the inheritance prediction on the data available in the parental BAM files and allows for a fast and reliable selection of potential de novo variants.

AgED performs automatic feature extraction from your image data and allows for their visualization and management. AgED relies on Elliptic Fourier Transcriptors to extract features from large quantities of image data. These features can then be visualized and you can evaluate them in a statistical manner. This type of analysis is particularly worthwile in the assessment of biological experiments. Elliptic Fourier Descriptors have been applied in a large range of applications in...

Cascading and Sharing Survival Trees (CSST) is a tree-based enseble that allows to efficiently analize survival data. It is a strightforward extension of the CS4 method for lifetime collections of data. The CSST software comes along with its companion the CSST Prediction tool, to use the ensemble prediction in everyday life. Please, refer to the user's manual for further information.

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bint was written for the purpose of obtaining subsets of intensity data from genotyping assays. Either the X & Y intensities for creating cluster plots or Log R Ratio and B Allele Frequencies for CNV detection. Extracting the data for individual SNP/CNV markers or individual samples was slow grep/awk'ing the text files exported from the genotyping run (e.g. Illumina final report files). bint converts the text representation of the intensity float data to into a IEEE754 indexed binary file...

The TRF-pathway package implements the powerful two-stage random forest based pathway analysis. The manuscript discussing the method is currently under revision at PLoS One.

The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.

LutefiskXP is ANSI C compliant software used to perform de novo peptide sequencing from tandem mass spectra.

This project will enable a research lab using Non-Human Primates to control and track the Non-Human primates and the experiments associated with each.

A Sequenced Binaural Wave Generator for Linux+Windows. May be used to generate sounds that entrain the brain's waves to oscillate at selected frequencies to aid in relaxation, lucid dreaming, meditation, clear thought, out-of-body experiences + more

balaBLAST is a free useful tool for the parallel execution of NCBI BLAST. It exploits I/O parallelism and database partitioning, while guaranteeing the same output reporting of a single-core NBCI BLAST. Really easy to install, with package Debian.

A rule-based modelling framework for allosteric proteins and biochemical networks.

Software for the visualization, analysis, and scoring of electrophysiological data.

CAMBIUM is a mathematically well-defined process language whose semantics are defined by operator algebras. It can function as a multi-paradigm intermediate representation for structure-altering models in developmental biology.

BSmapper - Sequence mapper for bisulfite sequencing reads for DNA methylation studies. Can handle Sanger and 454 reads for mapping to whole genomes or target regions.

MASyV (Multi-Agent System Visualization) enables one to write agent-based models/cellular automata, eg. in C, visualize them in real time & capture to movie file with MASyVs GUI & message passing lib. Includes examples: Hello World, ants, viral infection

A C++ Library for modelling and analyzing biochemical networks

HOPPscore is a simple application for evaluating the structural quality of theoretical or experimental protein structures. Protein are evaluated by comparing structure fragments to a reference dictionary of fragments from high resolution structures.

Piraña is a flexible modeling environment NONMEM and PsN.

DASS-GUI is a graphical user interface for pattern search in non-sequential data.

EMBOSS is a dynamic and comprehensive Open Source package for bioinformatics (DNA and protein sequence analysis, protein structure, phylogenetics, etc.). EMBOSS is written in C, also compatible with C++, and has a separate Java interface (Jemboss)