The package generates a feature table from a batch of LC/MS spectra in .cdf format. Instructions: http://www.sph.emory.edu/apLCMS/ References Bioinformatics. 25(15):1930-36. BMC Bioinformatics. 11:559.
R packages for PK/PD modeling, BE/BA, drug stability, ivivc, etc.
These R packages are developed for data analysis of PK/PD modeling, bioequivalence/bioavailability (BE/BA), drug stability, in-vitro and in-vivo correlation (ivivc), as well as therapeutic drug monitoring (TDM). They include bear, ivivc, PKfit, stab and tdm.
Units for computational cybernetics
CyberUnits is a cross-platform class library for rapid development of high-performance computer simulations in life sciences. It supports modelling for biomedical cybernetics and systems biology with Object Pascal, S and Matlab.
Event studies in several statistical packages
Software to perform event studies in several statistical packages, such as SAS, Stata and R.
NppToR provides R auto-completion and code passing between Notepad++ a
Similar to the windows R gui built in editor, NppToR aims to extend the functionality of code passing to the Notepad++ code editor. In addition to passing to the R gui, NppToR provides optional passing to a PuTTY window for passing to an R instance a remote machine. Easy shortcuts are also provided for easy batch execution, with a monitor for longer running scripts.
The new site is at http://psychometricon.net/libirt/
The new site is at http://psychometricon.net/libirt/ Library of functions to estimate the items and abilities from the responses of subjects to a questionnaire. The IRT models supported are the logistic model, the multivariate logistic model, the graded model and smoothing by penalization and kernel.
The Life Cycle Assessment Spreadsheet allows you to calculate carbon footprints and other environmental impacts for given product systems. Use requires basic skills in LCA and matrix algebra, but rewards effort with professional analytical tools.
R package for hierarchical species distribution models
hSDM is an R package for hierarchical species distribution models. Such models allows interpreting the observations (occurrence and abundance of a species) as a result of several hierarchical processes including ecological processes (habitat suitability, spatial dependence and anthropogenic disturbance) and observation processes (species detectability). Hierarchical species distribution models are essential for accurately characterizing the environmental response of species, predicting their probability of occurrence, and assessing uncertainty in the model results.
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 not hesitate to contact us in the forum or by email. Please see the original manuscript: Lopes, TJS, et al. (2015) - "Identifying problematic drugs based on the characteristics of their targets" - Frontiers in Pharmacology doi: 10.3389/fphar.2015.00186
A graphical user interface to R for use in Clinical Chemistry
This project is a graphical user interface to the R statistical programming language designed for use in Clinical Chemistry. It allows the user to perform Passing Bablok, Deming and Linear Regression and to produce high quality images in any file format for publication. The front end is written in Python 3.3 and PyQt4 and the form was designed using Qt4 Designer. The statistical analysis is written in R. The compiled binary was made with cx_freeze. This software is free and open-source. It is released under the GNU Public license and comes with absolutely no warranty.
R code/package for virus small RNA sequence data
For R 2.x please use version 0.7 or below For R 3.x please use version 0.8 and above viRome: an R package for the visualization and analysis of viral small RNA sequence datasets
User Friendly Data Analysis Tool for Interaction Data
TOPS provides the benchtop scientist with a free toolset to analyze, filter and visualize data from functional genomic gene-gene and gene-drug interaction screens with a flexible interface to accommodate various different technologies and analysis algorithms in addition to those already provided here.
YANG (Yet Another Network Generator - Java) enables you to generate social networks given various social rules observed in the real population. Uses: generate realistic networks to be used in individual-centric models, teaching or benchmarking.
Development of a common open source tool for assessing the accuracy of parameter estimates collected within the framework of the DCR (EU Regulation 1639/2001 and 1581/2004)
We have moved, the project is now at https://github.com/jlaake/mrds
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 and Binomial logistic regression models with variable time-intervals between land-cover observations. The two functions use embedded Gibbs samplers written in C++ with the Scythe statistical library to reduce computational time.
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 existing and simulated encounter data for other programs. SimAssem, along with the open source code, will hopefully give researchers and managers a tool for assessing the development of new estimators and evaluating potential decisions in a simulated environment. More information on SimAssem is given in Chapter 2, 'SimAssem: a program for simulating species assemblages and estimating species richness', in the dissertation 'Simulating species assemblages and evaluating species richness estimators'.
R package for analysis of ichthyoplanckton data. Please visit the ichthyoanalysis WIKI for more information and for collaboration
DynaMo (Dynamic Models) is a package for simulation, estimation, inference, regularization and prediction of time series models, with a special focus on the families of models used in Financial Econometrics.
Xpose - an S/R based population PK/PD model building aid for NONMEM.
FunctSNP is an R interface to an SQL database for linking single nucleotide polymorphisms (SNPs) to functional knowledge. FunctSNP should work on any OS on which R runs.
Structlab is a machine learning C++ framework for structured domains, which provides a toolbox of learning methods and tools for preprocessing and visualization. It also provides a GUI to setup elaborate experiments in a visual and intuitive way.
The project focuses on an relibility package for GNU R, which allows to estimate software reliability metrics like failure rate or hazard rate.
Visualisation of gene expression data on prokaryotic genomes
EnviroR is group of packages for the R Environment for Statistical Computing that provides data analysis and graphics tools for researchers and practitioners in the Earth and Environmental Sciences.