This package provides basic functionality for labeling iso- & anisotropic percolation clusters on 2D & 3D square lattices with various lattice sizes, occupation probabilities, von Neumann & Moore (1,d)-neighborhoods, and random variables weighting the percolation lattice sites.

This package provides a bioinformatics tool for the estimation of the tumor purity from sequencing data. It uses the set of putative clonal somatic single nucleotide variants within copy number neutral segments to call tumor cellularity.

This estimates precise weaning ages for a given skeletal population by analyzing the stable nitrogen isotope ratios of them. Bone collagen turnover rates estimated anew and the approximate Bayesian computation (ABC) were adopted in this package.

The package provides different distances measurements to calculate the difference between genesets. Based on these scores the genesets are clustered and visualized as graph. This is all presented in an interactive Shiny application for easy usage.

Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination.

The HiTC package was developed to explore high-throughput "C" data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided.

This package provides functions for kernel-regression-based association tests including Burden test, SKAT and SKAT-O. These methods aggregate individual SNP score statistics in a SNP set and efficiently compute SNP-set level p-values.

This package lets you construct paths to your project's files. Use the here function as a drop-in replacement for file.path, it will always locate the files relative to your project root.

This package provides SNP array data from different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.

Reaver performs a brute force attack against an access point's Wi-Fi Protected Setup (WPS) PIN. Once the PIN is found, the WPA passphrase can be recovered and the AP's wireless settings can be reconfigured.

This package provides methods for estimating online robust reduced-rank regression. The Gaussian maximum likelihood estimation method is described in Johansen, S. (1991) <doi:10.2307/2938278>. The majorisation-minimisation estimation method is partly described in Zhao, Z., & Palomar, D. P. (2017) <doi:10.1109/GlobalSIP.2017.8309093>. The description of the generic stochastic successive upper-bound minimisation method and the sample average approximation can be found in Razaviyayn, M., Sanjabi, M., & Luo, Z. Q. (2016) <doi:10.1007/s10107-016-1021-7>.

An implementation of a number of Global Trend models for time series forecasting that are Bayesian generalizations and extensions of some Exponential Smoothing models. The main differences/additions include 1) nonlinear global trend, 2) Student-t error distribution, and 3) a function for the error size, so heteroscedasticity. The methods are particularly useful for short time series. When tested on the well-known M3 dataset, they are able to outperform all classical time series algorithms. The models are fitted with MCMC using the rstan package.

An implementation of EDM algorithms based on research software developed for internal use at the Sugihara Lab ('UCSD/SIO'). The package is implemented with Rcpp wrappers around the cppEDM library. It implements the simplex projection method from Sugihara & May (1990) <doi:10.1038/344734a0>, the S-map algorithm from Sugihara (1994) <doi:10.1098/rsta.1994.0106>, convergent cross mapping described in Sugihara et al. (2012) <doi:10.1126/science.1227079>, and, multiview embedding described in Ye & Sugihara (2016) <doi:10.1126/science.aag0863>.

REAPER is a digital audio production application offering multitrack audio and MIDI recording, editing, processing, mixing and mastering toolset. It supports a vast range of hardware, digital formats and plugins, and can be comprehensively extended, scripted and modified.

Pair of simple convenience functions to convert a vector of birth dates to age and age distributions. These functions may be helpful when related age and custom age distributions are desired given a vector of birth dates.

Fast tool to calculate the Adjusted Market Inefficiency Measure following Tran & Leirvik (2019) <doi:10.1016/j.frl.2019.03.004>. This tool provides rolling window estimates of the Adjusted Market Inefficiency Measure for multiple instruments simultaneously.

Connectome Predictive Modelling (CPM) (Shen et al. (2017) <doi:10.1038/nprot.2016.178>) is a method to predict individual differences in behaviour from brain functional connectivity. cpmr provides a simple yet efficient implementation of this method.

Estimate the direct and indirect (mediation) effects of treatment on the outcome when intermediate variables (mediators) are compositional and high-dimensional. Sohn, M.B. and Li, H. (2017). Compositional Mediation Analysis for Microbiome Studies. (AOAS: In revision).

An implementation of calls designed to collect and organize in an easy way the data from the Steam API specifically for the Counter-Strike Global Offensive Game (CS Go) <https://developer.valvesoftware.com/wiki/Steam_Web_API>.

Given a collection of intervals with integer start and end positions, find recurrently targeted regions and estimate the significance of finding. Randomization is implemented by parallel methods, either using local host machines, or submitting grid engine jobs.

Tissue-specific enrichment analysis to assess lists of candidate genes or RNA-Seq expression profiles. Pei G., Dai Y., Zhao Z. Jia P. (2019) deTS: Tissue-Specific Enrichment Analysis to decode tissue specificity. Bioinformatics, In submission.

This package implements the de-biased estimator for low-rank matrix completion and provides confidence intervals for entries of interest. See: by Chen et al. (2019) <doi:10.1073/pnas.1910053116>, Mai (2021) <arXiv:2103.11749>.

This package provides a wrapper for the API of the Danish Parliament. It makes it possible to get data from the API easily into a data frame. Learn more at <http://www.ft.dk/dokumenter/aabne_data>.

Server implementation of GraphQL <http://graphql.github.io/graphql-spec/>, a query language originally created by Facebook for describing data requirements on complex application data models. Visit <http://graphql.org> to learn more about GraphQL'.