BASiCS is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments (where the groups of cells of interest are known a priori. BASiCS performs built-in data normalisation (global scaling) and technical noise quantification (based on spike-in genes). BASiCS provides an intuitive detection criterion for highly (or lowly) variable genes within a single group of cells. Additionally, BASiCS can compare gene expression patterns between two or more pre-specified groups of cells.

This package implements methods for batch correction and integration of scRNA-seq datasets, based on the Seurat anchor-based integration framework. In particular, STACAS is optimized for the integration of heterogeneous datasets with only limited overlap between cell sub-types (e.g. TIL sets of CD8 from tumor with CD8/CD4 T cells from lymphnode), for which the default Seurat alignment methods would tend to over-correct biological differences. The 2.0 version of the package allows the users to incorporate explicit information about cell-types in order to assist the integration process.

Streaming JSON (ndjson) has one JSON record per-line and many modern ndjson files contain large numbers of records. These constructs may not be columnar in nature, but it is often useful to read in these files and "flatten" the structure out to enable working with the data in an R data.frame-like context. Functions are provided that make it possible to read in plain ndjson files or compressed (gz) ndjson files and either validate the format of the records or create "flat" data.table structures from them.

Detection of rare aberrant splicing events in transcriptome profiles. Read count ratio expectations are modeled by an autoencoder to control for confounding factors in the data. Given these expectations, the ratios are assumed to follow a beta-binomial distribution with a junction specific dispersion. Outlier events are then identified as read-count ratios that deviate significantly from this distribution. FRASER is able to detect alternative splicing, but also intron retention. The package aims to support diagnostics in the field of rare diseases where RNA-seq is performed to identify aberrant splicing defects.

Interface package for sala', the spatial network analysis library from the depthmapX software application. The R parts of the code are based on the rdepthmap package. Allows for the analysis of urban and building-scale networks and provides metrics and methods usually found within the Space Syntax domain. Methods in this package are described by K. Al-Sayed, A. Turner, B. Hillier, S. Iida and A. Penn (2014) "Space Syntax methodology", and also by A. Turner (2004) <https://discovery.ucl.ac.uk/id/eprint/2651> "Depthmap 4: a researcher's handbook".

This package provides a tool for analyzing conjoint experiments using Bayesian Additive Regression Trees ('BART'), a machine learning method developed by Chipman, George and McCulloch (2010) <doi:10.1214/09-AOAS285>. This tool focuses specifically on estimating, identifying, and visualizing the heterogeneity within marginal component effects, at the observation- and individual-level. It uses a variable importance measure ('VIMP') with delete-d jackknife variance estimation, following Ishwaran and Lu (2019) <doi:10.1002/sim.7803>, to obtain bias-corrected estimates of which variables drive heterogeneity in the predicted individual-level effects.

Extends multiverse package (Sarma A., Kale A., Moon M., Taback N., Chevalier F., Hullman J., Kay M., 2021) <doi:10.31219/osf.io/yfbwm>, which allows users perform to create explorable multiverse analysis in R. This extension provides an additional level of abstraction to the multiverse package with the aim of creating user friendly syntax to researchers, educators, and students in statistics. The mverse syntax is designed to allow piping and takes hints from the tidyverse grammar. The package allows users to define and inspect multiverse analysis using familiar syntax in R.

This package provides tools for motif analysis in multi-level networks. Multi-level networks combine multiple networks in one, e.g. social-ecological networks. Motifs are small configurations of nodes and edges (subgraphs) occurring in networks. motifr can visualize multi-level networks, count multi-level network motifs and compare motif occurrences to baseline models. It also identifies contributions of existing or potential edges to motifs to find critical or missing edges. The package is in many parts an R wrapper for the excellent SESMotifAnalyser Python package written by Tim Seppelt.

This package provides a flexible framework for power analysis using Monte Carlo simulation for settings in which considerations of the correlations between predictors are important. Users can set up a data generative model that preserves dependence structures among predictors given existing data (continuous, binary, or ordinal). Users can also generate power curves to assess the trade-offs between sample size, effect size, and power of a design. This package includes several statistical models common in environmental mixtures studies. For more details and tutorials, see Nguyen et al. (2022) <arXiv:2209.08036>.

This package provides a comprehensive, user-friendly package for label-free proteomics data analysis and machine learning-based modeling. Data generated from MaxQuant can be easily used to conduct differential expression analysis, build predictive models with top protein candidates, and assess model performance. promor includes a suite of tools for quality control, visualization, missing data imputation (Lazar et. al. (2016) <doi:10.1021/acs.jproteome.5b00981>), differential expression analysis (Ritchie et. al. (2015) <doi:10.1093/nar/gkv007>), and machine learning-based modeling (Kuhn (2008) <doi:10.18637/jss.v028.i05>).

Bayesian Markov chain Monte Carlo (MCMC) estimation of spatial panel data models including Spatial Autoregressive (SAR), Spatial Durbin Model (SDM), Spatial Error Model (SEM), Spatial Durbin Error Model (SDEM), and Spatial Lag of X (SLX) specifications with fixed effects. Supports convex combinations of multiple spatial weight matrices and Bayesian Model Averaging (BMA) over subsets of weight matrices. Implements the convex combination spatial weight matrix methodology of Debarsy and LeSage (2021) <doi:10.1080/07350015.2020.1840993> and the Bayesian spatial panel data models of LeSage and Pace (2009, ISBN:9781420064247).

This package implements the Shimazaki-Shinomoto method for optimizing the bin width of histograms and the bandwidth of kernel density estimators. The framework minimizes the expected Mean Integrated Squared Error (MISE) and supports both 1D and 2D distributions, fixed and locally adaptive estimators, bootstrap confidence intervals, and OpenMP'-accelerated C++ backends'. Ideally suited for time-dependent rate estimation and identifying intrinsic data structures. For more details see Shimazaki and Shinomoto (2007) <doi:10.1162/neco.2007.19.6.1503> and Shimazaki and Shinomoto (2010) <doi:10.1007/s10827-009-0180-4>.

Fits linear varying coefficient (VC) models, which assert a linear relationship between an outcome and several covariates but allow that relationship (i.e., the coefficients or slopes in the linear regression) to change as functions of additional variables known as effect modifiers, by approximating the coefficient functions with Bayesian Additive Regression Trees. Implements a Metropolis-within-Gibbs sampler to simulate draws from the posterior over coefficient function evaluations. VC models with independent observations or repeated observations can be fit. For more details see Deshpande et al. (2026) <doi:10.1214/24-BA1470>.

Warning: r128gain has been deprecated; the owner recommends using rsgain instead. It is kept here only because it's the only tagger I've found that does what I want -_-'

r128gain is a multi platform command line tool to scan your audio files and tag them with loudness metadata (ReplayGain v2 or Opus R128 gain format), to allow playback of several tracks or albums at a similar loudness level. r128gain can also be used as a Python module from other Python projects to scan and/or tag audio files.

The package alpine helps to model bias parameters and then using those parameters to estimate RNA-seq transcript abundance. Alpine is a package for estimating and visualizing many forms of sample-specific biases that can arise in RNA-seq, including fragment length distribution, positional bias on the transcript, read start bias (random hexamer priming), and fragment GC-content (amplification). It also offers bias-corrected estimates of transcript abundance in FPKM(Fragments Per Kilobase of transcript per Million mapped reads). It is currently designed for un-stranded paired-end RNA-seq data.

This package provides classes and functions for quality control, filtering, normalization and differential expression analysis of pre-processed `RNA-seq` data. Data can be imported from `SummarizedExperiment` as well as `matrix` objects and can be annotated from `BioMart`. Filtering for genes without too low expression or containing required annotations, as well as filtering for samples with sufficient correlation to other samples or total number of reads is supported. The standard normalization methods including cpm, rpkm and tpm can be used, and DESeq2` as well as voom differential expression analyses are available.

This software is meant to be used for classification of images of cell-based assays for neuronal surface autoantibody detection or similar techniques. It takes imaging files as input and creates a composite score from these, that for example can be used to classify samples as negative or positive for a certain antibody-specificity. The reason for its name is that I during its creation have thought about the individual picture as an archielago where we with different filters control the water level as well as ground characteristica, thereby finding islands of interest.

markeR is an R package that provides a modular and extensible framework for the systematic evaluation of gene sets as phenotypic markers using transcriptomic data. The package is designed to support both quantitative analyses and visual exploration of gene set behaviour across experimental and clinical phenotypes. It implements multiple methods, including score-based and enrichment approaches, and also allows the exploration of expression behaviour of individual genes. In addition, users can assess the similarity of their own gene sets against established collections (e.g., those from MSigDB), facilitating biological interpretation.

For studying recurrent disease and death with competing risks, comparisons based on the well-known cumulative incidence function can be confounded by different prevalence rates of the competing events. Alternatively, comparisons of the conditional distribution of the survival time given the failure event type are more relevant for investigating the prognosis of different patterns of recurrence disease. This package implements a nonparametric estimator for the conditional cumulative incidence function and a nonparametric conditional bivariate cumulative incidence function for the bivariate gap times proposed in Huang et al. (2016) <doi:10.1111/biom.12494>.

DataSHIELD is an infrastructure and series of R packages that enables the remote and non-disclosive analysis of sensitive research data. This package is the DataSHIELD interface implementation for Opal', which is the data integration application for biobanks by OBiBa'. Participant data, once collected from any data source, must be integrated and stored in a central data repository under a uniform model. Opal is such a central repository. It can import, process, validate, query, analyze, report, and export data. Opal is the reference implementation of the DataSHIELD infrastructure.

This package provides statistical methods to check if a parametric family of conditional density functions fits to some given dataset of covariates and response variables. Different test statistics can be used to determine the goodness-of-fit of the assumed model, see Andrews (1997) <doi:10.2307/2171880>, Bierens & Wang (2012) <doi:10.1017/S0266466611000168>, Dikta & Scheer (2021) <doi:10.1007/978-3-030-73480-0> and Kremling & Dikta (2024) <doi:10.48550/arXiv.2409.20262>. As proposed in these papers, the corresponding p-values are approximated using a parametric bootstrap method.

Launches a shiny based application for Nuclear Magnetic Resonance (NMR) data importation and Statistical TOtal Correlation SpectroscopY (STOCSY) analyses in a full interactive approach. The theoretical background and applications of the STOCSY method are described by Cloarec, O., Dumas, M. E., Craig, A., Barton, R. H., Trygg, J., Hudson, J., Blancher, C., Gauguier, D., Lindon, J. C., Holmes, E. & Nicholson, J. (2005) <doi:10.1021/ac048630x>. Spectral alignment follows the interval correlation optimized shifting method of Savorani, F., Tomasi, G. & Engelsen, S. B. (2010) <doi:10.1016/j.jmr.2009.11.012>.

Optimized for handling complex datasets in environmental and ecological research, this package offers functionality that is not fully met by general-purpose packages. It provides two key functions, summarize_data()', which summarizes datasets, and plot_means()', which creates plots with error bars. The plot_means() function incorporates error bars by default, allowing quick visualization of uncertainties, crucial in ecological studies. It also streamlines workflows for grouped datasets (e.g., by species or treatment), making it particularly user-friendly and reducing the complexity and time required for data summarization and visualization.

The official Trends in International Mathematics and Science Study (TIMSS) 2023 website provides Teacher Context Data Files for Grade 4 in RData format. However, the available data are presented solely as numerical values. This package transforms the numerical data into categorical variables, enabling clearer interpretation and reducing ambiguity in statistical analysis. The category labels are provided in Bahasa Indonesia. This initiative contributes to promoting the use of Bahasa Indonesia in programming, in line with its designation as one of the official languages of the United Nations. For more details see <https://timss2023.org/>.