Search Results for "bio-bwa" - Page 3

It is often necessary to smooth high frequency fluctuations out of data streams sequenced by time, position, etc. The 'smooth' utility applies such smoothing using the wavelet algorithm. This implementation of wavelet smoothing was optimized for use in a data stream. It was adapted from HMMSeg Wavelet.Java by Thomas E. Wilson, University of Michigan. HMMSeg Wavelet.Java was written by Andrew Hemmaplardh, University of Washington. http://noble.gs.washington.edu/proj/hmmseg/ ...

The Dynamic Multispecies Metabolic Modeling (DyMMM [dĭm]) framework is a mathematical modeling tool that integrates multiple constraint-based metabolic models into a single dynamic community metabolic model. The DyMMM framework was formerly known as the DMMM framework. Please use the following citation for bibliographical purposes: Zhuang, K., Izallalen, M., Mouser, P., Richter, H., Risso, C., Mahadevan, R., & Lovley, D. R. (2011). Genome-scale dynamic modeling of the competition...

MCPerm: A Monte Carlo permutation method for multiple test correlation in case-control association study Traditional permutation (TradPerm) test is an important non-parametric analysis method which can be treated as the gold standard for multiple testing corrections in case-control association study. However, it relies on the original single nucleotide polymorphism (SNP) genotypes and phenotypes data to perform a large number of random shuffles, and thus it is computationally intensive,...

This is a Matlab software package for single molecule FRET data analysis.

EToS (Efficient Technology of Spike sorting; Extracellular recording To Spike trains) is an open-source system for spike sorting. EToS contains the programs of spike detection, feature extraction and clustering.

The current software contains the implementation for the 454 pyrosequencing platform.

This software computes likelihoods for infinitely-many-sites sequence data under multiple merger coalescents. The likelihood can be computed exactly or approximated via importance sampling.

The final build of this software now is distributed in R, embedded in "RedeR': an R/Bioconductor package for hierarchical and nested network analysis... more about RedeR: http://bioconductor.org/packages/2.9/bioc/html/RedeR.html

gfit creates an interface between computational models and experimental data and provides tools for their analysis

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 population-based method for DNA copy number analysis: recurrent copy number aberration indentification in multiple samples (with no need of single-sample calling). Developed for a quick analysis of high resolution and large population data.

FastPval is multiple stage p-value computing software that computes empirical p-values from a large set of permutated/resampled background data.

An R package implementation of a consensus clustering methodology. This package allows users to perform re-sampling statistics based clustering using multiple clustering algorithms to assess the robustness of both clusters and members of clusters.

Fast search using a standard SQL on Oracle or PostgreSQL database. The package includes the database creator, loader and web application. It supports SMILES and SMARTS substructure searches, similarity search, stereochemistry.

Algorithms that optimally & efficiently map atomic reactions. See 1) Atomic Reaction Mapping {Crabtree: amazon, b&n} 2) J. of Exp. Algorithmics, Vol 13 {Crabtree, Mehta} 3) J. Chem. Inf. Model., 2010, 50 (9), pp 1751–1756 {Crabtree, Mehta, Kouri}.

An R package for detailed inspection and analysis of LCMS data. An R package developed by Sukhdeep Singh at Department of Surgery and Cancer, Imperial College London,UK.

This project has moved to http://code.google.com/p/synthetic/

Stand-alone software tool for the interactive CE analysis of microarray data. The software is a user-friendly and allows on-the-fly study of CE

An SQL handler to interface multiple databases data to the OpeNDAP Hyrax (BES) server. Written in C++, it uses unixODBC to query DB and can be dynamically extended to use proprietary ODBC API driver in many easy ways. It is bundled with scripts to ge

Parallelized (threaded) software to enumerate all maximal subgraphs of a graph that exceed a specified density, even if they overlap.

Opensource software projects for genetics and genomics from Sage Bionetworks.

The SNP ratio test can assess significance of enrichment of significant associations in genome-wide association studies. Tests can be applied to pathways such as KEGG/GO, or user-defined pathways to test specific hypotheses. See link below for more.

Software to cluster protein sequences into functionally similar groups. Journal reference: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/16/1765

An implementation of the Markovian Jensen Shannon divergence (MJSD). The code recursively segments a sequence of symbols and then assesses the divergence of each segment with respect to the entire sequence.

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.