Search Results for "smith statistical package" - Page 2
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Showing 62 open source projects for "smith statistical package"
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NanoR
R package built to analyze and compare Nanopore data
NanoR is a package for the statistical language and environment R, tested on Unix, MacOSX and Windows, that allows user-friendly analysis and comparison of 1D MinION and GridION X5 sequencing data within acceptable time frames. -
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JDistlib
Java library of statistical distribution
A Java package that provides routines for various statistical distributions. Based on R version 2.14.1 (continuously updated; current as of R v3.3.0). The major difference is that JDistlib is thread safe. The library contains the density (pdf), cumulative (cdf), quantile, and random number generator (RNG) routines of the following distributions: Ansari, Beta, Binomial, Cauchy, Chi square, Exponential, Fisher's F, Gamma, Geometric, Hypergeometric, Kendall, Logistic, Log normal, Negative binomial... -
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Peptrix
Label free peptide profiling
... database, which contains all metadata, such as experiment numbers and sample codes, 3) a FTP (File Transport Protocol) server to store all raw mass spectrometry files and processed data, 4) the software package R, which is used for modular statistical calculations, such as the Wilcoxon-Mann-Whitney rank sum test. -
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CamBA is a Linux package for statistical analysis, by script/GUI, of neuroimaging data (fMRI/sMRI), developed at the Brain Mapping Unit, University of Cambridge. Non-parametric permutation-based statistics. Input images: 4D NiFTI files, output: HTML/
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AKtoolbox
Matlab Toolbox for coevolution analysis of multiple sequence alignment
AK Toolbox is a Matlab Toolbox for co-evolution analysis for protein Multiple Sequence Alignment (MSA) distributed under Simplified BSD License. The aim of AK toolbox is to provide a set of Matlab functions, which are independent of Matlab Bioinforamtics Toolbox, for coevolution anaylsis for MSA. At present, co-evolution methods available in this package are Statistical Coupling Analysis (SCA), Explicit Likelihood of Subset Covariance (ELSC), Mutual Information (MI), Observed Minus Expected... -
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MSTgold
Estimate minimum spanning trees with statistical bootstrap support
Minimum spanning tree (MST) algorithms can generate multiple, equally-minimal, MSTs but MST programs typically report only one, arbitrarily chosen MST. Similarly, most MST programs do not provide statistical metrics to support the credibility of the MSTs that they estimate. MSTgold estimates the number of alternative MSTs, reports up to a user-determined number of those trees, reports a consensus tree, and implements a bootstrapping metric to assess the reliability of alternate MST... -
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REDO
REDO - RNA Editing Detection in Organelle
REDO is a comprehensive application tool for identifying RNA editing events in organelles based on variant call results (VCF files). It is a suite of Perl scripts and can work easily and directly in any operating system installed Perl and R Environment. The stringent rule depended filters and statistical filters are used in REDO for reducing false positive rate. It can provide detailed annotations, statistics and figures for RNA editing sites. REDO also can detect RNA editing events in multiple... -
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EDDA
Experiment Design for Differential Abundance Analysis
EDDA is a tool for systematic assessment of the impact of experimental design and the statistical test used on the ability to detect differential abundance. EDDA can aid in the design of a range of common experiments such as RNA-seq, ChIP-seq, Nanostring assays, RIP-seq and Metagenomic sequencing, and enables researchers to comprehensively investigate the impact of experimental decisions on the ability to detect differential abundance. More details of EDDA can be found at Luo, Huaien et al... -
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Salstat2
statistical package designed for the end user, multiplatform
Salstat2 is an statistical package written in python and designed for the end user It has a graphical user interface and also it is scriptable, It's multiplatform, It has a graphic system inherited from matplotlib, It allows you to use different libraries like numpy - for numerical calculations, it also lets you to interact with Microsoft Excel (R) by using a com client under windows(R) platform and finally you can create your own dialogs by using the interactive shell or the script panel. -
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StatAlign
An extendable statistical multiple alignment tool.
StatAlign is an extendable software package for Bayesian analysis of Protein, DNA and RNA sequences. Multiple alignments, phylogenetic trees and evolutionary parameters are co-estimated in a Markov Chain Monte Carlo framework, allowing for reliable measurement of the accuracy of the results. This approach eliminates common artifacts that traditional methods suffer from, at the cost of increased computational time. These artifacts include the dependency of the constructed phylogeny... -
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A collection of code, bundled into a single R package, to perform several aspects of data management, image pre-processing, data analysis and statistical inference related to the quantitative analysis of dynamic contrast-enhanced MRI (DCE-MRI).
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SalStat is a small application for statistical analysis emphasising the sciences and social sciences (particularly Psychology). The project is designed around the user interface which has been designed to be simple to use. Think SPSS, but better!
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EC2KEGG
Comparative analysis of enzyme lists
This is a perl-based package to perform comparative analysis of metabolic pathways between two organisms. The package takes as an input a reference organism and a list of enzymes (EC numbers). Then, it finds shared and unique enzymes and generates links to KEGG Pathways maps to highlight the overlaps. Statistical enrichment analysis is also provided. -
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phcfM
R package for modelling anthropogenic deforestation
phcfM is an R package for modelling anthropogenic deforestation. It was named after the REDD+ pilot-project 'programme holistique de conservation des forêts à Madagascar'. phcfM includes two main functions: (i) demography(), to model the population growth with time in a hierarchical Bayesian framework using population census data and Gaussian linear mixed models and (ii) deforestation(), to model the deforestation process in a hierarchical Bayesian framework using land-cover change data... -
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SimAssem
For processing and/or simulating species assemblage data.
SimAssem is a tool for investigating the performances of species richness estimators across widely ranging assemblages and survey designs. Assemblages are simulated by specifying the: 1) number of species, 2) total abundance of individuals, 3) abundance distribution, 4) spatial configuration, 5) species detection probabilities, 6) survey design, and 7) number of grid cells to survey (out of a square grid comprised of 10,000 cells). SimAssem also processes existing encounter data and formats... -
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OCEANS
Observational Cohort Event Analysis and Notification System
The toolbox was developed concurrently using C# and Java programming languages. This deployment strategy was designed to maximize compatibility and flexibility and allows continuous development and dissemination of statistical modules. The framework is a downloadable package that includes source code and assemblies/packages that can be plugged into projects in either programming environment to support retrospective and prospective static or automated real-time medical product surveillance. -
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EnvStats
An R Package for Environmental Statistics
EnvStats is an R package for environmental statistics. It is the open-source successor to the commercial module for S-Plus© called "EnvironmentalStats for S-Plus", which was first released in April, 1997. The EnvStats package, along with the R software environment, provides comprehensive and powerful software for environmental data analysis. EnvStats brings the major environmental statistical methods found in the literature and regulatory guidance documents into one statistical package, along... -
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GISBox by Citiviz
Ready-to-use appliance for GIS, Data Mining and Analysis, Modelling...
GISBox by Citiviz is a ready-to-use virtual appliance containing an assortment of powerful, free and open source GIS, Data Mining and Analysis, Modelling and Programming software and packages. The pre-configured and tested GISBox allows you to try and use in few minutes a variety of software used by data scientists, engineers, physicists, mathematicians, geomatics engineers, and geographers from around the globe, without installing anything more than once the Oracle VirtualBox™ software... -
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chart.asy
A convenience charting module for Asymptote
Asymptote is a powerful descriptive vector graphics language that provides a natural coordinate-based framework for technical drawing and can be downloaded from http://asymptote.sourceforge.net/ . This package comprises of three *.asy files that provide convenient plotting features to construct mean+/-S.E.M. bar charts, box and whiskers charts, and other statistical plots in both x and y axis directions. A number of routinely used statistical tests (e.g. t-test etc...) are also included. -
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basic-statistical-utilities-for-r
Various statistical utility functions for R.
Various utility functions that package common formulas for confidence intervals, tests of means, the Marascuilo test, sample size estimation, and other basic tasks. -
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mubiomics
Scripts for processing next-gen sequencing data
A set of scripts (mostly python) for processing reads generated by the Roche 454 or Illumina next-gen sequencing platforms. Included are quality control, read demultiplexing and microbiome characterisation scripts for use with usearch, pplacer and RDP classifier. The package was used to produce the data presented in Smith et al. (2012) "The Cervical Microbiome over 7 Years and a Comparison of Methods for its Characterization". -
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RSOAP is a SOAP interface for the open-source statistical package R. This permits software to access advanced statistical analysis techniques provided by R via the simple and widely accepted SOAP protocol. RSessionDA provides access to RSOAP for Zope.
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Maximum entropy is a powerful method for constructing statistical models of classification tasks, such as part of speech tagging in Natural Language Processing. Several example applications using maxent can be found in the OpenNLP Tools Library.
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This project adds a ribbon to excel with a number of statistical buttons. This is not intended to be a full statistical analysis package (like R), but only a source for quick visualizations and calculations. For Excel2007 and up
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OpenThermo
Statistical thermodynamics package
OpenThermo is a program package for statistical thermodynamics computations beyond rigid rotor - harmonic oscillator approximation