Search Results for "r package xmsannotator" - Page 7
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Showing 254 open source projects for "r package xmsannotator"
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sha3sum and then some
sha3sum - A demonstration of the Keccak permutation.
Hash mode interface to the Keccak code package. This program illustrates the use of the Keccak permutation. Usage is much more than a hash function. The NIST compatible settings are subject to change when they publish FIPS PUB 180-5. I wrote this program when evaluating the permutation and developing tree hashing for the Intel(R) MIC architecture. -
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bayescount
The bayescount R package
A set of functions to allow analysis of count data (such as faecal egg count data) using Bayesian MCMC methods. Returns information on the possible values for mean count, coefficient of variation and zero inflation (true prevalence) present in the data. A complete faecal egg count reduction test (FECRT) model is implemented, which returns inference on the true efficacy of the drug from the pre- and post-treatment data provided, using non-parametric bootstrapping as well as using Bayesian... -
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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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outbreaker
outbreaker
A R package for disease outbreak reconstruction using epidemiological and genetic data. -
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diggit
R package for DIGGIT algorithm
... interactomes (usually generated by the MINDy algorithm). Regulatory protein activity is inferred by the VIPER algorithm (available as an R package from bioconductor). -
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invertR
R package to identify inversions in Strand-seq data
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episerve
R-based server for infectious disease epidemiology
episerve is an R package providing functionalities for handling, visualizing and analyzing epidemics data through a R interface. -
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BeerFest DB
Beer festival cellar management database and related software.
The BeerFest DB project will be designed as a reusable software package to help organize beer festivals and record information concerning past events. Initially it will focus on tracking cask information (e.g., ordering, sales, quality control). -
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adegenet
an R package for the exploratory analysis of genetic and genomic data
an R package for the exploratory analysis of genetic and genomic data -
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BIOMOD2
biomod2 developing plateform
This version of biomod is not stable at time.. Plese refer to http://r-forge.r-project.org/R/?group_id=302 for the stable version of the package -
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ThermV
Comprehensive thermal analysis software package
ThermV thermal analysis software package aims to provide the most sophisticated automatic analysis of thermal analysis data (TG/DTG, DTA and DSC). It offers new algorithm for concurrent peak deconvolution at different heating rates and provides full kinetic analysis of these data, including isoconversional methods for Ea, determination of reaction model and full kinetic triplet, Avrami coefficients, and dimensionality of crystal growth for reactions in the solid state. The project... -
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TIDES
Taylor series Integrator for Differential Equations
Taylor series Integrator for Differential EquationS. This software is developed by Profs. A. Abad, R. Barrio, F. Blesa and M. Rodriguez, (GME, University of Zaragoza, Spain). It consists on a C (Fortran) library, libTIDES, and a Mathematica package, MathTIDES. (MathTIDES requires Mathematica version >= 7.0) . Basic references: * A. Abad, R. Barrio, F. Blesa, M. Rodriguez, 2012. Algorithm 924: TIDES, a Taylor series Integrator for Differential EquationS, ACM TOMS. 39, no. 1, art. 5. (Main... -
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SpeciesGeoCoder is an open-source software package written in Python and R, that utilise the GDAL library (http://www.gdal.org/) for fast analysis of geoTIFF files, which allows for the easy and fast coding of species into user-defined operational units. For more info: https://github.com/mtop/speciesgeocoder
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miRNA Temporal Analyzer (mirnaTA)
Differential expression analysis tool for miRNAs in temporal studies
The microRNA Temporal Analyzer (mirnaTA) is a bioinformatics tool which can be used to identify differentially expressed miRNAs in temporal studies. It is implemented in Perl and R package (>= 2.13.0) and can be run across multiple platforms such as Linux, Mac and Windows. The mirnaTA requires that users provide data from a minimum of two time points and analyze up to 20 time points. To normalize data and remove technical variability, Normal Quantile Transformation (NQT) was used... -
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GenomicVis
Genomic data visualisation
GenomicVis is a R package that contains a collection of function for the visualisation of genomic data typically derived from high-throughput whole genome sequencing and SNP-Chip experiments. Most of the functions provided by this package are agnostic about where the data actually comes from, that is, they required input in simple data.frame instances that are not tied to a particular file format; however, we also provide many examples of creating these simply data.frames from standard file... -
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MSPrep
MS Prep R Package
R package for post processing of metabolomic data. Performs summarization of replicates, filtering, imputation, normalization, generates diagnostic plots and outputs final analytic datasets for downstream analysis -
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netClass is an R package for network-based feature (gene) selection for biomarkers discovery via integrating biological information. This package adapts the following 5 algorithms for classifying and predicting gene expression data using prior knowledge: 1) average gene expression of pathway (aep); 2) pathway activities classification (PAC); 3) Hub network classification (hubc); 4) filter via top ranked genes (FrSVM); 5) network smoothed t-statistic (stSVM).
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twoe
Modelling tropical forest dynamics
‘twoe’ (2e) is a software which aims first, at estimating the demographic parameters of tropical tree species from permanent forest plot data (through an R package) and second, at simulating forest dynamics (through a Capsis module). Authors: Ghislain Vieilledent, François de Coligny. -
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BBER
BBER: Bicluster-based Error Rate Control for eQTL Analysis
R Package for BBER: Bicluster-based Error Rate Control for eQTL Analys. This is an alternative repository for the package while it is being processed into Bioconductor. -
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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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ADRminer
An R package for the automated generation of drug safety signals
Adverse Drug event Reporting systems miner -
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RIPE (Regulatory network Inference from joint Perturbation and Expression data) is a novel three-step method that integrates both perturbation data and steady state gene expression data in order to estimate a regulatory network. The ripe package is written in R, with additional functionality provided by a MATLAB executable file. The executable file uses a runtime engine called the MATLAB Compiler Runtime (MCR). The executable for different architectures is distributed on this site together...
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WATSpackage
R package for acoustic-assisted whale survey simulation
WATS is an R package (>R2.15) whose main purpose is to run an individual-based simulation of an acoustically-assisted mark-recapture survey of whales Version 1.0 = for R2.15.x Version 1.01 = for R3.0.3+ For details see: Peel D, Miller BS, Kelly N, Dawson S, Slooten E and Double MC (2014) A simulation study of acoustic-assisted tracking of whales for mark-recapture surveys. PloSOne in press. -
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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...