Helper functions for descriptive tasks such as making print-friendly bivariate tables, sample size flow counts, and visualizing sample distributions. Also contains R approximations of some common SAS and Stata functions such as PROC MEANS from SAS and ladder', gladder', and pwcorr from Stata'.

Flexible implementation of a structural change point detection algorithm for multivariate time series. It authorizes inclusion of trends, exogenous variables, and break test on the intercept or on the full vector autoregression system. Bai, Lumsdaine, and Stock (1998) <doi:10.1111/1467-937X.00051>.

This package provides a suite of tools to allow you to download all publicly available parasite rate survey points, mosquito occurrence points and raster surfaces from the Malaria Atlas Project <https://malariaatlas.org/> servers as well as utility functions for plotting the downloaded data.

Transactions occurring for a UK-based and registered, non-store online retail between 01/12/2010 and 09/12/2011 (Chen et. al., 2012, <doi:10.1145/1835804.1835882>). This dataset is included in this package with the donor's permission, Dr. Daqing Chen.

This package provides function for performing Bayesian survival regression using Horseshoe prior in the accelerated failure time model with log normal assumption in order to achieve high dimensional pan-cancer variable selection as developed in Maity et. al. (2019) <doi:10.1111/biom.13132>.

This package draws protein schematics from Uniprot API output. From the JSON returned by the GET command, it creates a dataframe from the Uniprot Features API. This dataframe can then be used by geoms based on ggplot2 and base R to draw protein schematics.

GSALightning provides a fast implementation of permutation-based gene set analysis for two-sample problem. This package is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is necessary for more accurate p-values estimation.

This package implements bindings for SQL tables that are compatible with Bioconductor S4 data structures, namely the DataFrame and DelayedArray. This allows SQL-derived data to be easily used inside other Bioconductor objects (e.g., SummarizedExperiments) while keeping everything on disk.

This package provides a set of tools built around updateObject() to work with old serialized S4 instances. The package is primarily useful to package maintainers who want to update the serialized S4 instances included in their package. This is still work-in-progress.

This package lets you fit generalized linear mixed models for a single grouping factor under maximum likelihood approximating the integrals over the random effects with an adaptive Gaussian quadrature rule; Jose C. Pinheiro and Douglas M. Bates (1995) <doi:10.1080/10618600.1995.10474663>.

This package performs two-sample comparisons using the restricted mean survival time (RMST) when survival curves end at different time points between groups. This package implements a sensitivity approach that allows the threshold timepoint tau to be specified after the longest survival time in the shorter survival group. Two kinds of between-group contrast estimators (the difference in RMST and the ratio of RMST) are computed: Uno et al(2014)<doi:10.1200/JCO.2014.55.2208>, Uno et al(2022)<https://CRAN.R-project.org/package=survRM2>, Ueno and Morita(2023)<doi:10.1007/s43441-022-00484-z>.

RegLog system provides a set of shiny modules to handle register procedure for your users, alongside with login, edit credentials and password reset functionality. It provides support for popular SQL databases and optionally googlesheet-based database for easy setup. For email sending it provides support for emayili and gmailr backends. Architecture makes customizing usability pretty straightforward. The authentication system created with shiny.reglog is designed to be optional: user don't need to be logged-in to access your application, but when logged-in the user data can be used to read from and write to relational databases.

This package defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. It provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users.

Enables gene regulatory network (GRN) analysis on single cell clusters, using the GRN analysis software ANANSE', Xu et al.(2021) <doi:10.1093/nar/gkab598>. Export data from Seurat objects, for GRN analysis by ANANSE implemented in snakemake'. Finally, incorporate results for visualization and interpretation.

This package creates pre- and post- intervention scattergrams based on audiometric data. These scattergrams are formatted for publication in Otology & Neurotology and other otolaryngology journals. For more details, see Gurgel et al (2012) <doi:10.1177/0194599812458401>, Oghalai and Jackler (2016) <doi:10.1177/0194599816638314>.

The goal of equatiomatic is to reduce the pain associated with writing LaTeX formulas from fitted models. The primary function of the package, extract_eq(), takes a fitted model object as its input and returns the corresponding LaTeX code for the model.

Human names are complicated and nonstandard things. Humaniformat, which is based on Anthony Ettinger's humanparser project (https://github.com/ chovy/humanparser) provides functions for parsing human names, making a best- guess attempt to distinguish sub-components such as prefixes, suffixes, middle names and salutations.

Manipulates invertible functions from a finite set to itself. Can transform from word form to cycle form and back. To cite the package in publications please use Hankin (2020) "Introducing the permutations R package", SoftwareX, volume 11 <doi:10.1016/j.softx.2020.100453>.

This package provides beginner friendly framework to analyse population genetic data. Based on adegenet objects it uses knitr to create comprehensive reports on spatial genetic data. For detailed information how to use the package refer to the comprehensive tutorials or visit <http://www.popgenreport.org/>.

Fast multi-trait and multi-trail Genome Wide Association Studies (GWAS) following the method described in Zhou and Stephens. (2014), <doi:10.1038/nmeth.2848>. One of a series of statistical genetic packages for streamlining the analysis of typical plant breeding experiments developed by Biometris.

Annotation files of the formatted genomic annotation for ChromHMM. Three types of text files are included the chromosome sizes, region coordinates and anchors specifying the transcription start and end sites. The package includes data for two versions of the genome of humans and mice.

Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.

This package provides delayed computation of a matrix of scaled and centered values. The result is equivalent to using the scale function but avoids explicit realization of a dense matrix during block processing. This permits greater efficiency in common operations, most notably matrix multiplication.

This package defines S4 classes for single-cell genomic data and associated information, such as dimensionality reduction embeddings, nearest-neighbor graphs, and spatially-resolved coordinates. It provides data access methods and R-native hooks to ensure the Seurat object is familiar to other R users.