This package provides a wrapper for the homologene database by the National Center for Biotechnology Information (NCBI). It allows searching for gene homologs across species. The package also includes an updated version of the homologene database where gene identifiers and symbols are replaced with their latest (at the time of submission) version and functions to fetch latest annotation data to keep updated.

This package provides functionality to compute various node centrality measures on networks. Included are functions to compute betweenness centrality (by utilizing Madduri and Bader's SNAP library), implementations of Burt's constraint and effective network size (ENS) metrics, Borgatti's algorithm to identify key players, and Valente's bridging metric. The betweenness, Key Players, and bridging implementations are parallelized with OpenMP.

This gem provides beautiful console logging for Ruby applications. It implements fast, buffered log output and has the following features:

• Thread safe global logger with per-fiber context

• Carry along context with nested loggers

• Enable/disable log levels per class

• Detailed logging of exceptions

• Beautiful logging to the terminal or structured logging using JSON.

This package is a tool to predict the power of CyTOF experiments in the context of differential state analyses. The package provides a shiny app with two options to predict the power of an experiment: i. generation of in-sicilico CyTOF data, using users input ii. browsing in a grid of parameters for which the power was already precomputed.

The CTexploreR package re-defines the list of Cancer Testis/Germline (CT) genes. It is based on publicly available RNAseq databases (GTEx, CCLE and TCGA) and summarises CT genes main characteristics. Several visualisation functions allow to explore their expression in different types of tissues and cancer cells, or to inspect the methylation status of their promoters in normal tissues.

This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also implemented.

"LipidTrend" is an R package that implements a permutation-based statistical test to identify significant differences in lipidomic features between groups. The test incorporates Gaussian kernel smoothing of region statistics to improve stability and accuracy, particularly when dealing with small sample sizes. This package also includes two plotting functions for visualizing significant tendencies in 1D and 2D feature data, respectively.

This package provides tools to measure connection and independence between variables without relying on linear models. Includes functions to compute Eta squared, Chi-squared, and Cramer V. The main advantage of this package is that it works without requiring parametric assumptions. The methods implemented are based on educational material and statistical decomposition techniques, not directly on previously published software or articles.

This package provides a simple approach to measure political sophistication based on open-ended survey responses. Discursive sophistication captures the complexity of individual attitude expression by quantifying its relative size, range, and constraint. For more information on the measurement approach see: Kraft, Patrick W. 2023. "Women Also Know Stuff: Challenging the Gender Gap in Political Sophistication." American Political Science Review (forthcoming).

It contains functions for dose calculation for different routes, fitting data to probability distributions, random number generation (Monte Carlo simulation) and calculation of systemic and carcinogenic risks. For more information see the publication: Barrio-Parra et al. (2019) "Human-health probabilistic risk assessment: the role of exposure factors in an urban garden scenario" <doi:10.1016/j.landurbplan.2019.02.005>.

Simplex optimization algorithms as firstly proposed by Spendley et al. (1962) <doi:10.1080/00401706.1962.10490033> and later modified by Nelder and Mead (1965) <doi:10.1093/comjnl/7.4.308> for laboratory and manufacturing processes. The package also provides tools for graphical representation of the simplexes and some example response surfaces that are useful in illustrating the optimization process.

This package provides a collection of methods for commonly undertaken analytical tasks, primarily developed for Public Health Scotland (PHS) analysts, but the package is also generally useful to others working in the healthcare space, particularly since it has functions for working with Community Health Index (CHI) numbers. The package can help to make data manipulation and analysis more efficient and reproducible.

This package implements the Quantification Evidence Standard algorithm for computing Bayesian evidence sufficiency from binary evidence matrices. It provides posterior estimates, credible intervals, percentiles, and optional visual summaries. The method is universal, reproducible, and independent of any specific clinical or rule based framework. For details see The Quantitative Omics Epidemiology Group et al. (2025) <doi:10.64898/2025.12.02.25341503>.

Doubly-robust, non-parametric estimators for the transported average treatment effect from Rudolph, Williams, Stuart, and Diaz (2023) <doi:10.48550/arXiv.2304.00117> and the intent-to-treatment average treatment effect from Rudolph and van der Laan (2017) <doi:10.1111/rssb.12213>. Estimators are fit using cross-fitting and nuisance parameters are estimated using the Super Learner algorithm.

Estimate and return either the traffic speed or the car entries in the city of Thessaloniki using historical traffic data. It's used in transport pilot of the BigDataEurope project. There are functions for processing these data, training a neural network, select the most appropriate model and predict the traffic speed or the car entries for a selected time date.

The wavelet and ANN technique have been combined to reduce the effect of data noise. This wavelet-ANN conjunction model is able to forecast time series data with better accuracy than the traditional time series model. This package fits hybrid Wavelet ANN model for time series forecasting using algorithm by Anjoy and Paul (2017) <DOI: 10.1007/s00521-017-3289-9>.

This package provides a not uncommon task for quants is to create waterfall charts'. There seems to be no simple way to do this in ggplot2 currently. This package contains a single function (waterfall) that simply draws a waterfall chart in a ggplot2 object. Some flexibility is provided, though often the object created will need to be modified through a theme.

emacs-ranger is a minor mode that runs within dired, it emulates many of ranger's features. This minor mode shows a stack of parent directories, and updates the parent buffers, while you're navigating the file system. The preview window takes some of the ideas from Peep-Dired, to display previews for the selected files, in the primary dired buffer.

Modern results of psychometric theory are implemented to provide users with a way of evaluating the internal structure of a set of items guided by theory. These methods are discussed in detail in VanderWeele and Padgett (2024) <doi:10.31234/osf.io/rnbk5>. The relative excess correlation matrices will, generally, have numerous negative entries even if all of the raw correlations between each pair of indicators are positive. The positive deviations of the relative excess correlation matrix entries help identify clusters of indicators that are more strongly related to one another, providing insights somewhat analogous to factor analysis, but without the need for rotations or decisions concerning the number of factors. A goal similar to exploratory/confirmatory factor analysis, but recmetrics uses novel methods that do not rely on assumptions of latent variables or latent variable structures.

This package provides exploratory data analysis methods to summarize, visualize and describe datasets. The main principal component methods are available, those with the largest potential in terms of applications: principal component analysis (PCA) when variables are quantitative, correspondence analysis (CA) and multiple correspondence analysis (MCA) when variables are categorical, Multiple Factor Analysis when variables are structured in groups, etc. and hierarchical cluster analysis.

Build complex HTML or LaTeX tables using kable() from knitr and the piping syntax from magrittr. The function kable() is a light weight table generator coming from knitr. This package simplifies the way to manipulate the HTML or LaTeX codes generated by kable() and allows users to construct complex tables and customize styles using a readable syntax.

Rxvt-unicode (urxvt) is a colour vt102 terminal emulator intended as an xterm replacement for users who do not require features such as Tektronix 4014 emulation and toolkit-style configurability. It supports unicode, XFT and may be extended with Perl plugins. It also comes with a client/daemon pair that lets you open any number of terminal windows from within a single process.

Computes Multiple Co-Inertia Analysis (MCIA), a dimensionality reduction (jDR) algorithm, for a multi-block dataset using a modification to the Nonlinear Iterative Partial Least Squares method (NIPALS) proposed in (Hanafi et. al, 2010). Allows multiple options for row- and table-level preprocessing, and speeds up computation of variance explained. Vignettes detail application to bulk- and single cell- multi-omics studies.

TADCompare is an R package designed to identify and characterize differential Topologically Associated Domains (TADs) between multiple Hi-C contact matrices. It contains functions for finding differential TADs between two datasets, finding differential TADs over time and identifying consensus TADs across multiple matrices. It takes all of the main types of HiC input and returns simple, comprehensive, easy to analyze results.