Search Results for "c algorithms"

The ChIP-Seq software provides methods for the analysis of ChIP-seq data and other types of mass genome annotation data. The most common analysis tasks include positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-depleted regions.

This project, initially developed at University College London, contains programs to perform rigid, affine and non-linear registration of nifti or analyse images. Two versions of the algorithms are included, a CPU- and a GPU- (using CUDA) based implementation.

This site hosts the source code for C++ version of the Broker for SBW, NOM module, advanced simulation suite, analysis applications and model editors.

Clone-by-clone sequencing, as a means of achieving high quality assemblies for large and complex genomes, continues to be of great relevance in the era of high throughput sequencing. However, assemblies obtained using current whole genome assemblers are often fragmented and sometimes have issues of genome completeness owing to different data characteristics introduced by multiplexed sequencing. With iCAS the data filtering process is based on a novel kmer frequency algorithm, resulting...

FieldTrip is the Matlab toolbox for EEG and MEG data. It includes algorithms for simple and advanced analysis, such as importing, preprocessing, time-frequency analysis, source reconstruction, statistical testing and connectivity analysis.

The General Hidden Markov Model Library (GHMM) is a C library with additional Python bindings implementing a wide range of types of Hidden Markov Models and algorithms: discrete, continous emissions, basic training, HMM clustering, HMM mixtures.

...SOAP3-dp natively supports BAM file format and provides the same scoring scheme as BWA, which enables it to be integrated into existing analysis pipelines. Citation: Luo R, Wong T, Zhu J, Liu C-M, Zhu X, et al. (2013) SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner. PLoS ONE 8(5): e65632. doi:10.1371/journal.pone.0065632

Provides bitwise, context-based 2nd generation data compression for large FASTQ-based files

This library is a lightweight implementation of genetic algorithm, contains the most popular types of chromosomes and the basic algorithms for selection, elitism, crossing and mutation.

This is a C library with a set of functions that allow the user to evolve biological networks. The user provides a fitness function in C, and the library will do the rest. A few simulation algorithms and examples are included.

Palex is a two-stage biological sequence searching system. Library will contain functions for searching patterns, palindromes and structures in DNA sequence.

This is a C library for using genetic algorithms to evolve biological networks, specifically metabolic, signaling, and gene regulatory networks. Users must specify the fitness function and may override the other default functions.

The gsuffix library implements serveral algorithms used for enumerative string searches. It incorporates the suffix tree and suffix array data structures as well as some other methods.

ANT is a lightweight implementation in C of a kind of artificial neural net called Multilayer Perceptron, which uses the backpropagation algorithm as learning method. The package includes an introductory example to start using artificial neural nets.

A C++ library for Bayesian computation, including a collection of more generally-applicable utilities.

ea-fold is a platform to perform protein folding simulations by means of evolutionary algorithms. The program implements a parallelized distributed evolutionary algorithms and a flexible force field.

Multilayered feed-forward neural network software written in C++. Backpropagation and RPROP are available as training algorithms. Design goals: speed of execution when calculating the output to new data, and quality of training (preprocessing: PCA).

OLIGOMAP is a tool to help researchers engineer restriction sites into oligonucleotides using silent mutagenesis and reverse translation algorithms.