Search Results for "sensitivity" - Page 3
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Showing 83 open source projects for "sensitivity"
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ChelomEx
Isotope assisted discovery of metal chelating agents from LC-MS data
ChelomEx identifies chromatographic features of metal complexes and associated free ligands or other related adducts in high-resolution LC-MS data. A built-in graphical user interface and compound library aid in the efficient evaluation of the results. If you use ChelomEx for your research, please cite our Analytical Chemistry paper that describes the software (http://dx.doi.org/10.1021/ac503000e). To comment, send bug reports or suggestions for additional features to be implemented... -
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olego
OLego – short or long RNA-seq read mapping to discover exon junction
OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seeding and extension scheme, and does not rely on a separate external mapper. It achieves high sensitivity of junction detection by using very small seeds (12-14 nt), efficiently mapped using Burrows-Wheeler transform (BWT) and FM-index. This also makes it particularly sensitive for discovering small exons. It is implemented in C++ with full support of multiple threading, to allow fast processing of large-scale data. -
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NotesTyper
Convert your text typing into music
...When generating music all nuances of your typing are taken into account: what keys were pressed, exact timings of all key presses and key releases, velocity (loudness) of typing. Who can be interested: Researchers: experiment with converting text to music and explore fundamental relationships. Musicians: virtual keyboard with touch sensitivity. Music composers: compose new music with algorithmic and improvisation approach. Text authors: listen and share to how your text can sound. -
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chipexo
model based analysis of ChIP-exo data
...MACExo has the following four steps: 1) sequencing data normalization and bias correction; 2) signal consolidation and noise reduction; 3) single nucleotide resolution border detection using Chebyshev Inequality; and 4) border matching using Gale-Shapley’s stable matching algorithm. When applied to yeast Reb1 and human CTCF ChIP-exo data, MACE is able to define TFBSs with higher sensitivity, specificity and spatial resolution, as evidenced by multiple criteria, such as motif enrichment, sequence conservation, nucleosome positioning, and open chromatin states. -
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GESPA
Accurately predicts disease association of single nucleotide mutations
GESPA (GEnomic Single nucleotide Polymorphism Analyzer) is a bioinformatics tool for classifying Nonsynonymous Single Nucleotide Polymorphisms (nsSNPs). GESPA predicts if a nsSNP is pathogenic using reports from literature and various algorithms to assess conservation in orthologous and paralogous protein alignments. Using reports from literature, GESPA is also able to predict the phenotype of a nsSNP with high accuracy. The software can be used clinically to determine if observed nsSNPs are... -
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NGS_AMAS
All-Mapping tool using Adaptive Seeds
AMAS is designed to find all possible mapping locations of NGS reads in a reference genome with up to a given number of errors (mismatches+gaps). AMAS features an efficient and accurate strategy of partition and filtration of adaptive seeds to speed up the read mapping while preserving the sensitivity. -
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argument
Command line argument parser library for Java
Moved to GitHub https://github.com/fedups Command-line argument compiler and parser. With just two lines of code you can start to set up a command-line interface to your Java programs. Many advanced features including "required", "positional", "multiple", and the most advanced - "group" -
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TIDES
Taylor series Integrator for Differential Equations
...TIDES tutorial: Integrating ODEs by using the Taylor Series Method., Monografías de la Academia de Ciencias de la Universidad de Zaragoza. 36, pp. 1-116. * R. Barrio, 2005. Performance of the Taylor series method for ODEs/DAEs, Appl. Math. Comput. 163 (2), pp. 525--545 * R. Barrio, 2006. Sensitivity analysis of ODE's/DAE's using the Taylor series method, SIAM J. on Scientific Computing 27 (6), pp. 1929--1947 -
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simplex with branch and bound
A tool for teaching simplex and branch & bound methods
This is a tool for teaching simplex and branch & bound methods. For simplex method, it comes with several examples including degeneracy and cycling, and allow the user to dictate how to pivot. For branch and bound method, it is desinged to interact with the user to explore all possible branch and bound trees. The user can also load a problem from a text file or simply type in a model directly. The format is very simple and very similar to the LP format, see the packed-in examples. -
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...User has also option to choose between Gist and PHOG features to be used in both training and prediction module. This TB-Xpredict software is extremely efficient and having a maximum prediction accuracy of 94.2% with sensitivity of 0.961 for Gist features.
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TAMeBS
A sensitive bisulfite-sequencing read mapping tool
TAMeBS-0.4 is designed for mapping BS reads on to a reference genome and providing simple analysis of methylation status of each cytosine in genome. It has perfect capability to detect many more uniquely mapped reads that other existing tools while achieving an excellent balance between sensitivity and precision. The recent version works best for single-end BS reads generated from directional protocal. Moreover, insertion and deletion are not taken into account in the alignemnt process. -
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grasp-release
GRASP: Guided Reference-based Assembly of Short Peptides
...GRASP assembles the fragmented short-peptides, which are called from the NGS reads, and aligns the assembled contigs to the query reference protein. GRASP achieves much higher sensitivity than BLASTP for gene annotation purpose. If you found GRASP useful for your projects, please cite: Zhong, C., Yang, Y., and Yooseph, S. GRASP: Guided Reference-based Assembly for Short Peptides, Manuscript in preparation -
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FineSplice
Enhanced splice junction detection and estimation from RNA-Seq data
FineSplice is a Python wrapper to TopHat2 geared towards a reliable identification of expressed exon junctions from RNA-Seq data, at enhanced detection precision with small loss in sensitivity. Following alignment with TopHat2 using known transcript annotations, FineSplice takes as input the resulting BAM file and outputs a confident set of expressed splice junctions with the corresponding read counts. Potential false positives arising from spurious alignments are filtered out via a semi-supervised anomaly detection strategy based on logistic regression. ... -
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ABM-Calibration-SensitivityAnalysis
Codes and Data for Calibration and Sensitivity Analysis of ABM
Find here the model, code, and example results of parameter fitting/calibration and sensitivity analysis for an agent-based model using NetLogo and R. The corresponding manuscript is published in Journal of Artificial Societies and Social Simulation as: Thiele JC, Kurth W, Grimm V (2014): Facilitating parameter estimation and sensitivity analysis of agent-based models: a cookbook using NetLogo and R. <http://jasss.soc.surrey.ac.uk/xx/x/x.html> Methods/Techniques used are: a. ... -
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Sphinx SD Tools
Common accessible environment for system dynamics simulation.
The Sphinx project is dedicated to create common accessible environment for system dynamics simulation. This software is developed on Java 6 platform and use Java Swing GUI. -
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PIN
Provenance in NetLogo
This tool can trace, capture, query and visualize the dependency provenance in NetLogo. It consists of four main components: a source code analyzer used to automatically add probes to the model's source code, a NetLogo extension for capturing the provenance traces generated from probes, a non-preprocessing (NP) provenance slicing technique for computing provenance slices using provenance traces, and a visualization component for visualizing the provenance slices. It is compatible with... -
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Cake
A bioinformatic tools for somatic mutation discovery
Cake, a bioinformatics software pipeline that integrates four publicly available somatic variant-calling algorithms to identify single nucleotide variants with higher sensitivity and accuracy than any one algorithm alone. Cake can be run on a high-performance computer cluster or used as a stand-alone application For additional information on how to obtain and run Cake, updates and known issues please visit the wiki page https://sourceforge.net/p/cakesomatic/wiki/Cake%20Somatic/ -
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PseudoDomain
Accurate identification of pseudogenes without genome annotations
...Accurate identification of pseudogenes is important to understand biological and evolutionary histories of genomes and genes. PseudoDomain is a processed pseudogene identification tool with high sensitivity and low false positive rate. It can identify pseudogenes in species that do not have accurate genome annotations. In addition, it can accurately predict the number and positions of frameshifts within putative pseudogenes. -
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QSAR Qualitative Validation
Qualitative validation of QSAR models
The purpose of this program is to verify the ability of the QSAR/Pharmacophore model to distinguish significantly between the two classes (i.e. active and inactive molecules). It is based on calculation of different qualitative validation parameters such as sensitivity, specificity, precision, accuracy, and F-measure. -
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AirKey
Gesture mapping for the Leap Motion
CURRENT VERSION: AirKey v0.9 Simple program for Windows to utilize the gesture capabilities of the Leap Motion - check readme.txt. Feedback welcome, either here in the Discussion or at forums.leapmotion.com - http://bit.ly/1eT6TI8 An overview of the available gestures can be found at http://youtu.be/nyZ1yF2G_dQ There is also a very convenient configuration editor with a GUI available, created by Sharp: http://www.irishacts.com/misc/airkey-gui.exe, with an explanatory video at... -
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SPSens
Stochastic parameter sensitivity analysis for chemical networks
SPSens is a complete software package written in C that estimates parameter sensitivities for stochastic models of chemical and biochemical reaction networks using Monte Carlo (MC) stochastic simulations. It is possible to estimate sensitivities with respect to system parameters using the following algorithms: finite difference methods (crude monte carlo, common reaction path, coupled finite differences); likelihood ratio methods; and regularized pathwise derivatives. Additionally the... -
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Bis-SNP
Bisulfite-seq/NOMe-seq SNPs & cytosine methylation caller
...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 bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously. It works for both of single-end and paired-end reads.Specificity and sensitivity has been validate by Illumina IM SNP array. In default threshold (Phred scale score > 20), it could detect 92.21% heterozygous SNPs with 0.14% false positive rate (90.88% sensitivity in C/T SNPs with 0.16% false positive rate, 98.51% sensitivity in non C/T SNPs with 0.16% false positive rate). Cytosine calling is not only based on reference context, so it could detect non-reference cytosine context. -
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Software to solve Linear Programming problems applying the Revised Simplex Algorithm (2-Phase Method) and performing a Sensitivity Analysis too.
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PCASP Calibrator
Software for processing PCASP calibration data
...https://sourceforge.net/projects/opccalibrator/ PCASP Calibrator is software for processing calibration data from a PMS Passive Cavity Aerosol Spectrometer Probe with SPP-200 electronics. It provides a graphical user interface displaying plots of size distributions and sensitivity fits. Source code is included. This software includes data for common calibration materials, calculated using MieConScat (http://sourceforge.net/projects/mieconscat). This software can be used for generating data for other aerosol using Mie-Lorenz theory or the user can use their own software for another scattering theory. The metodologies used by this software are now published at, http://www.atmos-meas-tech.net/5/1147/2012/amt-5-1147-2012.html -
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