Search Results for "ghost 4 linux"
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Showing 66 open source projects for "ghost 4 linux"
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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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Hyperspectral data analysis in R
Handling and basic analysis of hyperspectral data in R
The hsdar package contains classes and functions to manage, analyse and simulate hyperspectral data. These might be either spectrometer measurements or hyperspectral images through the interface of rgdal. -
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pexm - JAGS module
JAGS module for the piecewise exponential distribution
This new module was built for users interested in a programming language similar to BUGS to fit a Bayesian model based on the piecewise exponential distribution. The module is an extension of the open-source program JAGS. The PE distribution is widely used in the fields of survival analysis and reliability. Currently, it can only be implemented in JAGS through methods to indirectly specify the likelihood based on the Poisson or Bernoulli probabilities. Our module provides a more... -
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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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biOP
biOP [bio~ObjectPascal/bio~Delphi] bioinformatics libraries
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An R package for metrology. metRology provides classes and calculation and plotting functions for metrology applications, including measurement uncertainty estimation and (eventually) inter-laboratory metrology comparison studies.
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bspipe
An End-to-End Analysis Pipeline for BS-seq
BSpipe is a comprehensive pipeline from sequence quality control and mapping to functional analysis of differentially methylated regions: (1) sequencing quality assessment, (2) sequence cleaning, (3) sequence read mapping, (4) methylation quantification, (4) sample comparisons based on methylation profile, (5) identification of DMRs (differentially methylated regions), (6) annotation of DMRs, (7) functional analysis of differentially methylated genes, (8) generation of input files... -
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TEACUP
TCP Experiment Automation Controlled Using Python
TEACUP automates many aspects of running TCP performance experiments in a specially-constructed physical testbed. TEACUP enables repeatable testing of different TCP algorithms over a range of emulated network path conditions, bottleneck rate limits and bottleneck queuing disciplines. TEACUP utilises a text-based configuration file to define experiments as combinations of parameters specifying desired network path and end host conditions. When multiple values are provided (e.g. for TCP... -
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Maui
Maui is the Maltcms User Interface
Maui is the Maltcms User Interface, a rich client application for Chromatography-Mass Spectrometry and related research areas. -
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We developed a systematic algorithmic solution for quantitative drug sensitivity scoring (DSS), based on continuous modeling and integration of multiple dose-response relationships in high-throughput compound testing studies. License: The DSS R-package is made available under the terms of the GNU General Public License, which means that the source code is freely available for use within other software, but if you alter the code and distribute it, you must make the new source code...
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SWire4R
An R package enabling R to interact with Stata for data exchange
Swire4R is an R package for exchanging data between R and Stata. SWire4R uses SWire for connecting R to Stata. SWire is a plugin for Stata >=13 which acts like a server: client applications can query SWire for interacting with Stata. SWire4R acts like a client application for Swire, providing the user with various basic functions for retrieving data from Stata and exporting data to Stata. SWire4R must be compiled by R. For more information about SWire, visit https://sourceforge.net/projects/swire/ -
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BayesRate
Bayesian estimation of diversification rates
BayesRate is a program to estimate speciation and extinction rates from dated phylogenies in a Bayesian framework. The methods are described in: Silvestro, D., Schnitzler, J. and Zizka, G. (2011) A Bayesian framework to estimate diversification rates and their variation through time and space. BMC Evolutionary Biology, 11, 311 Silvestro D., Zizka G. & Schulte K. (2014) Disentangling the effects of key innovations on the diversification of Bromelioideae (Bromeliaceae). Evolution, 68, 163-175. -
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Waterloo
Java-based scientific graphics
Java-based scientific graphics with support for Java, Groovy, MATLAB, Python, the R statistical environment, Scala and SciLab. -
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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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mRIN
Assessing mRNA integrity directly from RNA-Seq data
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This is an R package for the Mass spectrometry Research. The MrR can be used to analyze the mass spectrometry data for baseline correction, denoising, peak detection, peak alignment, peak normalization, and biomarker discovery.
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ncPRO-seq
Non-Coding RNA PROfiling from sRNA-seq
ncPRO-seq is a tool for annotation and profiling of ncRNAs from smallRNA sequencing data. It aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions in miRBase, piRBase, Rfam and repeatMasker, and regions defined by users. The ncPRO pipeline also has a module to identify regions significantly enriched with short reads that can not be classified as known ncRNA families. ############# Docker version : download and run Dockerfile (go in... -
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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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The Dataverse Network is a Java EE5 app that enables researchers to share data on-line. It provides data citation standards, facilitates preservation, distribution and replication of data, and includes statistical analysis. More at: http://thedata.org
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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)... -
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swathTUNER
Software tool for optimizing data-independent acquisition methods
SwathTUNER combines usability and flexibility for the selection of different SWATH data acquisition strategies to address the requirements of multiple experimental conditions. It can be used for any acquisition instrument, including FT-based analyzers, where the same principles with respect to variable precursor isolation windows apply. Fixed and variable windows based on equalizing the distribution of either the precursor ions or the total ion current within each window can be created. -
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The Protein Similarity Network
Human protein similarity network used to predict drug safety.
This is the protein similarity network - PSIN. Here, the nodes are human proteins and they are linked only if they share considerable sequence similarity. We found that this network is particularly useful to distinguish approved from problematic drug-targets. Here you also find the complete set of programs and datasets we used for this purpose. Free to help further test and develop this project. Your help and expertise are much appreciated ! If you have any questions, please do... -
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PS Matching in SPSS
Propensity score matching in SPSS
Propensity score matching in SPSS Provides SPSS custom dialog to perform propensity score matching. Using the SPSS-R plugin, the software calls several R packages, mainly MatchIt and optmatch. Proper citations of these R packages is provided in the program. -
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Toolchain for quantification of fluorescence intensity and morphological parameters in single cells using microscope based cytometry.
