Search Results for "bio toolkit"

Now in Github: https://github.com/dnaase/Bis-tools/tree/master/Bis-SNP BisSNP is a package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq and RRBS) on Illumina platform. It uses bayesian inference with either manually specified or automatically estimated methylation probabilities of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other...

The Maltcms - Modular Application Toolkit for Chromatography Mass-Spectrometry is a JAVA API for preprocessing, alignment, analysis and visualization of data stored in open file formats used in Proteomics and Metabolomics research.

KAnalyze is a Java toolkit designed to convert DNA and RNA sequences into k-mers. It is both a command line application and an API.

The Bamformatics project aims to provide a coherent and consistent approach to analysis of high-throughput sequencing data. Its toolkit includes, among others, programs to identify variants and to compute various types genomic tracks. It also provides a graphical user interface to facilitate general bioinformatic workflows. The project wiki contains further details.

Toolkit for processing genetic data. Currently supports (command-line): Half-IBD (Identity by descent) aka HIRs - between 2 or any number of files (in distances and cM); RAW2PED, PED2RAW conversions; regions of homozygousity and other converters.

.... The first homepage tab links to our pipeline constructer. The second homepage tab links to a xterm session on the client. Software included (location - name): path - biobambam path - bwa path - bowtie2 path - bowtie path - cufflinks path - bcftools path - tophat path - scalpel path - samtools path - sra-toolkit path - bamtools path - delly path - delly-parallel path - picard-tools path - fastahack path - twoBitToFa ~/prog/java/ - mutect ~/prog/python/ - platypus ~/prog/java/ - gatk

Toolkit to examine the topology of a phylogenetic tree, place amino acid substitutions on specific branches, polarize them and compare amino acid sequences of homologous proteins to answer a wide range of questions about protein evolution.

For comparative plus/minus spreadsheet data, Coulson Plot Generator application creates a multiple pie diagram, for a rapid visual comparison of subunit occupancy across a range of entities. Numbers of pies, segments, labels and colours are customisable. Creates an editable PDF from a comma separated text file. Now with zoom capability and more memory, for larger datasets. Save images in several formats including SVG.

The BioNLP UIMA Component Repository provides UIMA wrappers for novel and well-known 3rd-party NLP tools used in biomedical text prosessing, such as tokenizers, parsers, named entity taggers, and tools for evaluation.

AJT is a set of utility classes for Java for handling some bioinformatics data, graphics file export, GUI widgets, and classes that should long have been added to the official Java API.

FishingCNV, a software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. The inputs are standard coverage files produced by Genome Analysis ToolKit (GATK), and the output is a file containing putative CNVs. The program comes in 2 different releases * GUI version (FishingCNV_X.X.X.zip) * Command line version (FishingCNV_X.X_pipeline) Browse through our files to find the different releases.

The JPL project is no longer updated and maintained. It has evolved after being completely reengineered and upgraded. The new project is available at http://mzjava.expasy.org.

An integrated bioinformatics toolkit for analysis of ChIPseq data from the Illumina DNA sequencing platform. Includes filtering, quality control, simulation, peakfinding, visualization, and comparison of samples.

PileLine (Pileup pipeLine) is a toolkit for efficient handling of genomic position (GP) files, produced by next-generation sequencing experiments. It is designed to be memory efficient by performing on-disk operations over sorted GP files.

Object oriented reusable software classes designed to be used to construct larger software projects developed in multiple software languages.

A tool to construct the metabolic networks from KEGG, and compare the constructed metabolic networks. Phylogenetic trees can be constructed along the case.

The Xholon project explores: software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.

This is a java open source package for analyzing bio-data. We build this project as an inititive for people interested in bio-informatic to share new ideas and publish their innovative methods.

This Project moved to https://sourceforge.net/projects/synbiowave/ because the name GeneWave is a registered trademark... Please do not use this project anymore.

Genome Data Visualization Toolkit (GDVTK) is a Java library for building bioinformatics visualization application. See Bioinformatics, 2004 Mar 22;20(5):727-34. Java-based application framework for visualization of gene regulatory region annotations.

A plugin package for ImageJ that assists with quantification and characterization of vascular networks. The tool regularizes lighting, segments the vessels, and generates a skeletal description that reflects the biological structures of interest.

This software system serves as both a DICOM image viewer as well as a diagramming tool for collaborating notes on the given image sets. This my Computer Science graduate thesis project at Loyola Marymount University.

Tools for comparative sequence analysis. Includes FamilyRelations (GUI) and a C++ toolkit/Python wrapper for doing fixed-width-window analyses.

Java/XML toolkit for research using Bayesian networks and other graphical models of probability (exact and approximate inference, structure learning, etc.)

EOS stands for Entity Oriented Search. The project is a toolkit to support EOS projects on a Lucene and Hadoop platform.