Search Results for "jancox-tools"
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Showing 36 open source projects for "jancox-tools"
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PANDA
A comprehensive and flexible quantification tool for proteomics data
PANDA is a comprehensive and flexib tool for quantitative proteomics data analysis, which is developed based on our solid foundations in quantitative proteomics for years. Several novelties have been implemented in it. First, we implement the advantage algorithms of LFQuant (Proteomics 2012, 12, (23-24), 3475-84) and SILVER (Bioinformatics 2014, 30, (4), 586-7) into PANDA. Second, we consider the state-of-art concept of quantification reliability in this quantitative workflow. On the levels... -
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TXM
Unicode-XML-TEI text/corpus analysis platform
TXM is a free and open-source cross-platform Unicode & XML based text/corpus analysis environment and graphical client, supporting Windows, Linux and Mac OS X. It can also be used online as a J2EE standard compliant web portal (GWT based) with access control built in. DOWNLOAD LATEST VERSION OF TXM : http://textometrie.ens-lyon.fr/spip.php?rubrique61&lang=en TXM offers a comprehensive range of analysis tools (concordances, collocate search, frequency lists, etc.) based on the powerfull... -
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The application Bio7 is an integrated development environment for ecological modelling and contains powerful tools for model creation, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.
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mzMatch is a Java collection of small commandline tools specific for metabolomics MS data analysis. The tools are built on top of the PeakML core library, providing mass spectrometry specific functionality and access to the PeakML file format.
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timetools (for r-cran)
Seasonal/Sequential (Instants/Durations, Even or not) Time Series
... to daily time series for instance) are also defined. Tools provided can be used for instance to handle environmental monitoring data (not always produced on a regular time base). -
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We are developing data standards and software tools that implement these standards to develop a systemic approach to modeling, capturing, analyzing and disseminating flow cytometry data.
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Computer programs for application in Sports science, Physical Culture, among others. By Enrique R.P. Buendía Lozada. buendiaenr@gmail.com , Benemérita Universidad Autónoma de Puebla (BUAP), México. (Software without any warranty).
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Mass-Up
MALDI-TOF data analysis tool
Mass-Up is an Open-Source mass spectrometry utility for proteomics designed to support the preprocessing and analysis of MALDI-TOF mass spectrometry data. Mass-Up includes several tools and operations to load, preprocess and analyze MALDI-TOF data. -
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AMEN (Annotation, Mapping, Expression and Network) is a stand-alone, unified suite of tools to manage, explore and combine biological multifaceted high-throughput data such as annotation, chromosomal location, expression and interaction data.
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TEACUP
TCP Experiment Automation Controlled Using Python
... congestion control algorithm), an experiment is made up of multiple tests. For each experiment and test, TEACUP collects a range of data, such as tcpdump files of traffic seen or TCP stack information (e.g. using Web10G). TEACUP also collects a variety of metadata from the end hosts and bottleneck router, such as the actual OS/kernel version(s) used. TEACUP also provides some simple tools for analysing the results of experiments, such as plotting a flow's experienced RTT over time. -
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Ship Lock Scheduling
Scheduling lockages at ship locks with several parallel lock chambers
This Java software includes algorithms of combinatorical optimization for the NP-hard offline ship lock scheduling problem. Solutions and performed computations can be displayed graphically. Besides, there is a framework for generating test instances and running these in parallel, as well as R/JGR code for statistical evaluation. Some tools for estimating the quality of calculated solutions will be further improved. Initially the software was developed within a project of TU Berlin regarding... -
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Corbata
CORe microBiome Analysis Tools
Corbata is a set of statistical tools that can be used to analyze the core microbiome across a set of samples. -
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##### The RKWard project has moved! ##### Find the most recent news and downloads at http://rkward.kde.org . RKWard aims to provide an easily extensible, easy to use IDE/GUI for R. RKWard tries to combine the power of the R-language with the (relative) ease of use of commercial statistics tools.
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NOFI ranking
The Non-Outlier Fragment Ion ranking for enhaced DIA quantification
The NOFI ranking algorithm has been developed to assign low priority to fragment ions affected by interference. The implementation is an R script that can be customized. A future version will contain a modular version. The outline is as follows: 1) The input contains the list of SWATH fragment ion XICs from the identified and quantified peptides by software tools such as Skyline and OpenSWATH. 2) The first step in NOFI is the computation of the 4 attributes (RTd, FWHMd, IRd and IRrep) used... -
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R-gregmisc is a set of extension package for the open-source statistical environment/language "R''. It includes functions for plotting (gplots), data manupulation (gdata), modeling (gmodels), and programming tools (gtools), creation and management of sub-processes (fork), determing sample sizes for -omics experiments (ssize), and a variety of other packages.
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iMir
Integrated pipeline for HT miRNA-Seq data analysis
Processing of smallRNA-Seq data to gather biologically relevant information requires application of multiple statistical and bioinformatics tools from different sources, each focusing on a specific step of the analysis pipeline. The analytical workflow can be challenging for the continuous interventions by the operator, a critical factor when large numbers of datasets need to be analyzed at once. To allow a flexible and comprehensive analysis of smallRNA-Seq data we designed a novel modular... -
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An implementation of the Kernel-based Orthogonal Projections to Latent Structures (K-OPLS) method for MATLAB and R. The supplied functionality includes e.g. cross-validation, kernel parameter optimization, model diagnostics and plot tools.
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NGSbinningpytools
Python tools for binning NGS scaffolds to various genomes.
Next generation sequencing has opened new avenues for sequencing prokaryotes which were difficult or either impossible to culture. Now, it is possible to sequence all organisms present in a metagenomic community. However, a critical problem is to determine the host organism for each genomic fragment present in the dataset. This project provides the computational tools for assigning the organismal identity for each genomic scaffold in the given dataset. For more detailed documentation please... -
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EnvStats
An R Package for Environmental Statistics
... with an extensive hypertext help system that explains what these methods do, how to use these methods, and where to find them in the environmental statistics literature. Also included are numerous built-in data sets from regulatory guidance documents and the environmental statistics literature. EnvStats combined with other R packages (e.g., for spatial analysis) provides the environmental scientist, statistician, researcher, and technician with tools to “get the job done!” -
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R Unit test framework R functions implementing a standard Unit Testing framework, with additional code inspection and report generation tools
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imDEV
Tools for multivariate data visualization, exploration and analysis.
You may also like some newer work: http://createdatasol.com/ Project imDEV is an application of RExcel, which seamlessly integrates Excel and R for tasks focused on multivariate data visualization, exploration, and analysis. Interactive modules for dimensional reduction (imPCA), prediction (imPLS), feature selection, analysis of correlation (imCorrelations) and generation of networked structures (imGraph) provide an integrated environment for systems level analysis of multivariate data. -
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Electrophysiology & circular stats tools
Data analysis and circular statistics with OpenElectrophy and R
Set of tools for basic analysis of electrophysiological data. The Python classes show how to call OpenElectrophy functions and save data. The R library applies circular statistics to spike phase data and saves the best von Mises fit and the Rayleigh statistics on the disk. The wavelet coherence analysis is done in R by the package "sowas". Check the module R_coherence to see how we solved that problem. This packages may be useful for people who start using OpenElectrophy and circular... -
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ANDES. This is a library and a set of applications that can be used to analyze the results of deep sequencing results. (See Li et al.: ANDES: Statistical tools for the ANalyses of DEep Sequencing. BMC Research Notes 2010 3:199.)
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Chipster is a biologist-friendly analysis software for high-throughput data. It contains over 200 analysis tools for next generation sequencing (NGS), microarray and proteomics data. Users can combine tools in automatic analysis workflows, which can be shared. Chipster's interactive visualizations allow users to select datapoints and create new gene lists. For NGS data Chipster contains a built-in genome browser, which highlights SNPs and automatically indexes BAM files and calculates coverage...