In tumor tissue, underlying genomic instability can lead to DNA copy number alterations, e.g., copy number gains or losses. Sporadic copy number alterations occur randomly throughout the genome, whereas recurrent alterations are observed in the same genomic region across multiple independent samples, perhaps because they provide a selective growth advantage. Here we use cyclic shift permutations to identify recurrent copy number alterations in a single cohort or recurrent copy number differences in two cohorts based on a common set of genomic markers. Additional functionality is provided to perform downstream analyses, including the creation of summary files and graphics. DiNAMIC.Duo builds upon the original DiNAMIC package of Walter et al. (2011) <doi:10.1093/bioinformatics/btq717> and leverages the theory developed in Walter et al. (2015) <doi:10.1093/biomet/asv046>. An article describing DiNAMIC.Duo by Walter et al. (2022) can be found at <doi: 10.1093/bioinformatics/btac542>.

An RStudio addin for teaching and learning data manipulation using the dplyr package. You can learn each steps of data manipulation by clicking your mouse without coding. You can get resultant data (as a tibble') and the code for data manipulation.

S4-classes for setting up a coherent framework for simulation within the distr family of packages.

This package provides external JAR dependencies for the DatabaseConnector package.

Given the non-negative data and its distribution, the package estimates the rank parameter for Non-negative Matrix Factorization. The method is based on hypothesis testing, using a deconvolved bootstrap distribution to assess the significance level accurately despite the large amount of optimization error. The distribution of the non-negative data can be either Normal distributed or Poisson distributed.

Summarizes data frames by calculating various statistics including central tendency, dispersion, shape, and normality diagnostics. Handles numeric, character, and factor columns with NA-aware computations.

Several functions are provided for dose-response (or concentration-response) characterization from omics data. DRomics is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of replicates). DRomics provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive a benchmark dose or concentration and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data in log2, RNAseq data in raw counts, or already pretreated continuous omics data (such as metabolomic data) in log scale. In order to link responses across biological levels based on a common method, DRomics also handles apical data as long as they are continuous and follow a normal distribution for each dose or concentration, with a common standard error. For further details see Delignette-Muller et al (2023) <DOI:10.24072/pcjournal.325> and Larras et al (2018) <DOI:10.1021/acs.est.8b04752>.

Fit latent variable linear models, estimating score distributions for groups of people, following Cohen and Jiang (1999) <doi:10.2307/2669917>. In this model, a latent distribution is conditional on students item response, item characteristics, and conditioning variables the user includes. This latent trait is then integrated out. This software is intended to fit the same models as the existing software AM <https://am.air.org/>. As of version 2, also allows the user to draw plausible values.

Fits Gaussian Mixtures by applying evolution. As fitness function a mixture of the chi square test for distributions and a novel measure for approximating the common area under curves between multiple Gaussians is used. The package presents an alternative to the commonly used Likelihood Maximization as is used in Expectation Maximization. The algorithm and applications of this package are published under: Lerch, F., Ultsch, A., Lotsch, J. (2020) <doi:10.1038/s41598-020-57432-w>. The evolution is based on the GA package: Scrucca, L. (2013) <doi:10.18637/jss.v053.i04> while the Gaussian Mixture Logic stems from AdaptGauss': Ultsch, A, et al. (2015) <doi:10.3390/ijms161025897>.

Utilities to represent, visualize, filter, analyse, and summarize time-depth recorder (TDR) data. Miscellaneous functions for handling location data are also provided.

Joint DNA-based disaster victim identification (DVI), as described in Vigeland and Egeland (2021) <doi:10.21203/rs.3.rs-296414/v1>. Identification is performed by optimising the joint likelihood of all victim samples and reference individuals. Individual identification probabilities, conditional on all available information, are derived from the joint solution in the form of posterior pairing probabilities. dvir is part of the pedsuite collection of packages for pedigree analysis.

This package performs the identification of differential risk hotspots (Briz-Redon et al. 2019) <doi:10.1016/j.aap.2019.105278> along a linear network. Given a marked point pattern lying on the linear network, the method implemented uses a network-constrained version of kernel density estimation (McSwiggan et al. 2017) <doi:10.1111/sjos.12255> to approximate the probability of occurrence across space for the type of event specified by the user through the marks of the pattern (Kelsall and Diggle 1995) <doi:10.2307/3318678>. The goal is to detect microzones of the linear network where the type of event indicated by the user is overrepresented.

While it has been well established that drugs affect and help patients differently, personalized drug response predictions remain challenging. Solutions based on single omics measurements have been proposed, and networks provide means to incorporate molecular interactions into reasoning. However, how to integrate the wealth of information contained in multiple omics layers still poses a complex problem. We present a novel network analysis pipeline, DrDimont, Drug response prediction from Differential analysis of multi-omics networks. It allows for comparative conclusions between two conditions and translates them into differential drug response predictions. DrDimont focuses on molecular interactions. It establishes condition-specific networks from correlation within an omics layer that are then reduced and combined into heterogeneous, multi-omics molecular networks. A novel semi-local, path-based integration step ensures integrative conclusions. Differential predictions are derived from comparing the condition-specific integrated networks. DrDimont's predictions are explainable, i.e., molecular differences that are the source of high differential drug scores can be retrieved. Our proposed pipeline leverages multi-omics data for differential predictions, e.g. on drug response, and includes prior information on interactions. The case study presented in the vignette uses data published by Krug (2020) <doi:10.1016/j.cell.2020.10.036>. The package license applies only to the software and explicitly not to the included data.

Compute the dynamic threshold panel model suggested by (Stephanie Kremer, Alexander Bick and Dieter Nautz (2013) <doi:10.1007/s00181-012-0553-9>) in which they extended the (Hansen (1999) <doi: 10.1016/S0304-4076(99)00025-1>) original static panel threshold estimation and the Caner and (Hansen (2004) <doi:10.1017/S0266466604205011>) cross-sectional instrumental variable threshold model, where generalized methods of moments type estimators are used.

This package implements S4 classes for probability models based on packages distr and distrEx'.

Density ratio estimation. The estimated density ratio function can be used in many applications such as anomaly detection, change-point detection, covariate shift adaptation. The implemented methods are uLSIF (Hido et al. (2011) <doi:10.1007/s10115-010-0283-2>), RuLSIF (Yamada et al. (2011) <doi:10.1162/NECO_a_00442>), and KLIEP (Sugiyama et al. (2007) <doi:10.1007/s10463-008-0197-x>).

Classical Test and Item analysis, Item Response analysis and data management for educational and psychological tests.

DataSHIELD is an infrastructure and series of R packages that enables the remote and non-disclosive analysis of sensitive research data. This DataSHIELD Interface implementation is for analyzing datasets living in the current R session. The purpose of this is primarily for lightweight DataSHIELD analysis package development.

Helpers functions to process, analyse, and visualize the output of single locus species delimitation methods. For full functionality, please install suggested software at <https://legallab.github.io/delimtools/articles/install.html>.

Curated datasets and intuitive data management functions to streamline epidemiological data workflows. It is designed to support researchers in quickly accessing clean, structured data and applying essential cleaning, summarizing, visualization, and export operations with minimal effort. Whether you're preparing a cohort for analysis or creating reports, DIVINE makes the process more efficient, transparent, and reproducible.

Efficient estimation of Dynamic Factor Models using the Expectation Maximization (EM) algorithm or Two-Step (2S) estimation, supporting datasets with missing data. Factors are assumed to follow a stationary VAR process of order p. The estimation options follow advances in the econometric literature: either running the Kalman Filter and Smoother once with initial values from PCA - 2S estimation as in Doz, Giannone and Reichlin (2011) <doi:10.1016/j.jeconom.2011.02.012> - or via iterated Kalman Filtering and Smoothing until EM convergence - following Doz, Giannone and Reichlin (2012) <doi:10.1162/REST_a_00225> - or using the adapted EM algorithm of Banbura and Modugno (2014) <doi:10.1002/jae.2306>, allowing arbitrary patterns of missing data. The implementation makes heavy use of the Armadillo C++ library and the collapse package, providing for particularly speedy estimation. A comprehensive set of methods supports interpretation and visualization of the model as well as forecasting. Information criteria to choose the number of factors are also provided - following Bai and Ng (2002) <doi:10.1111/1468-0262.00273>.

Formatting of population and case data, calculation of Standardized Incidence Ratios, and fitting the BYM model using INLA'. For details see Brown (2015) <doi:10.18637/jss.v063.i12>.

The desirable Dietary Pattern (DDP)/ PPH score measures the variety of food consumption. The (weighted) score is calculated based on the type of food. This package is intended to calculate the DDP/ PPH score that is faster than traditional method via a manual calculation by BKP (2017) <http://bkp.pertanian.go.id/storage/app/uploads/public/5bf/ca9/06b/5bfca906bc654274163456.pdf> and is simpler than the nutrition survey <http://www.nutrisurvey.de>. The database to create weights and baseline values is the Indonesia national survey in 2017.

Simple Principal Components Analysis (PCA) and (Multiple) Correspondence Analysis (CA) based on the Singular Value Decomposition (SVD). This package provides S4 classes and methods to compute, extract, summarize and visualize results of multivariate data analysis. It also includes methods for partial bootstrap validation described in Greenacre (1984, ISBN: 978-0-12-299050-2) and Lebart et al. (2006, ISBN: 978-2-10-049616-7).