Search Results for "tools" - Page 2

tigreBrowser is a web-based browser for ranking results from R/Bioconductor package tigre and similar tools. It allows easy viewing, sorting and filtering of visualisations of models produced by tigre.

Tuque includes 4 programs: tuqueIndex to prepare Bowtie indexes that include spliced sequences tuqueMap to map reads using the prepared indices tuqueSplice to find splice junctions from the reads tuqueCount to count the reads mapping within annotated sequence intervals

...User can upload their raw signal intensities and will avail complete quality control of screen, hit selection, plotting of hit genes with gene ontology, comparing of replicates or comparing of channels. In addition, ScreenSifter has visualization tools to plot specific genes or gene groups in the screen data. ScreenSifter also provides Gene Set Enrichment Analysis (GSEA), protein-protein interaction directly on the plot. Publication: ScreenSifter: analysis and visualization of RNAi screening data Pankaj Kumar, Germaine Goh, Sarawut Wongphayak, Dimitri Moreau and Frédéric Bard BMC Bioinformatics. 2013 Oct 3;14(1):290. ...

SLiMScape adds Short linear motif discovery tools to Cytoscape, transforming it into a SLiM discovery platform. A tutorial is available at the following URL: http://bioware.ucd.ie/slimscape/

A set of very optimized tools for indexing/querying huge genomes/files. Provided so far: a very fast exact mapper, and an unconstrained split-mapper

This project incorporates a suite of tools that aim to allow researchers within Griffith's Imaging and Image Analysis Facility (GIIAF) to efficiently and effectively provide secure, centralised, web-accessible data storage, management and manipulation. The open-source Java-based OMERO software was customised to provide most of the features of this project.

metaProt is a python pipeline to analyze and extract data from protein sequences found in metagenomic projects. It integrates several existing tools (HMMer, Pepstats, Blast...) to be used against custom databases. Please, read the README.txt file to find more about this.

This is a c-library that provides tools for advanced analysis of electrophysiological data. It features denoising, unsupervised classification, time-frequency analysis, phase-space analysis, neural networks, time-warping and more.

The SplitDB project gives practitioners of statistical tools for inferring phylogenies a way to store, retrieve and visualize important properties, like convergence, of the overwhelmingly large resulting tree-sets produced by these tools.

--UPDATE-- New Version is now integrated in the official PyMOL plugin repository! --UPDATE-- The BNI (Beyond Normal Interaction)- Tools is a plug in for the PyMOL molecular visualization system which adds additional functionalities and presets to the PyMOL GUI and also adds useful extended commands.

A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.

Naimath (syn. blessing) is a project to create tools for diagnosis, management of clinical cases in the form of Rule based Medical Expert System integrating Interactive Health education, Semantified EMR, and serve as a learning tool for students. Website seen at www.naimath.com

A set of bioinformatics tools for the open source bio-informatics platform "birch"

At the outset, the goal of this program is to provide a suite of tools to aid in the back-translation of amino acid sequences in a manner that provides useful information for synthetic gene design.

A collection of tools for use in gene naming, including standardization, selection, and comparison.

Tools to perform metabolic control analyses on biochemical network models in SBML format. Allows computation of first and second order response coefficients, elasticities, first order control coefficients and first order spectral response coefficients.

DIY Genomics is an open source bioinformatics consortium intended to bring a collection of tools and libraries into the hands of small scale genomics labs for the process of sequence assembly and annotation. Projects include DIYA, MGAP, CRISPR, and DIYGV

Tools and programs I have written for various purposes and those used in it.

SeqFreed is a bioinformatics desktop. It provides efficient access to sequence data and gene features, a customizable command line interface to locally installed bioinformatic tools and flexible display of either text or images in different page modes.

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

Disease Gene Profiler (DGP) comprises of a set of (bioinformatics) tools that can be used to identify the genes underlying susceptibility to common multifactorial diseases (such as diabetes, asthma and cancer) using freely available datasources.

Path Sim contains a collection of tools for analysing Biochemical pathways with respect to stochastic behavior and cell-to-cell variations.

The purpose of this project is to make available a variety of tools written in Python.

The aim of our programm is to help lab on counting species and analyze the results with statistics tools.

Python module to interface mzML data in Python based on cElementTree with additional tools for MS-informatics. CITATION Please cite us when using pymzML for your publications. Bald, T., Barth, J., Niehues, A., Specht, M., Hippler, M., & Fufezan, C. (2012). pymzML - Python module for high throughput bioinformatics on mass spectrometry data. Bioinformatics, 1-2. doi: 10.1093/bioinformatics/bts066