This package provides a very bare-bones interface to use the Metropolis-Hastings Monte Carlo Markov Chain algorithm. It is suitable for teaching and testing purposes.
Penalized spatial median regression using LASSO. The iteratively reweighted least squares algorithm is used to solve the spatial median regression problem and weighted LASSO is employed.
Taxonomic information from Wikipedia', Wikicommons', Wikispecies', and Wikidata'. Functions included for getting taxonomic information from each of the sources just listed, as well performing taxonomic search.
Bundles the duckhts DuckDB extension for reading High Throughput Sequencing file formats with DuckDB'. The DuckDB C extension API <https://duckdb.org/docs/stable/clients/c/api> and its htslib dependency are compiled from vendored sources during package installation. James K Bonfield and co-authors (2021) <doi:10.1093/gigascience/giab007>. VariantKey / RegionKey support follows Nicola Asuni (2018) <doi:10.1101/473744>.
Building interactive web applications with R is incredibly easy with shiny'. Behind the scenes, shiny builds a reactive graph that can quickly become intertwined and difficult to debug. reactlog (Schloerke 2019) <doi:10.5281/zenodo.2591517> provides a visual insight into that black box of shiny reactivity by constructing a directed dependency graph of the application's reactive state at any time point in a reactive recording.
This package creates a muti-graph web page which allows the interactive exploration of differential analysis tests. The graphical web interface presents results as a table which is integrated with five interactive graphs: MA-plot, volcano plot, box plot, lines plot and cluster heatmap. Graphical aspect and information represented in the graphs can be customized by means of user controls. Final graphics can be exported as PNG format.
This package provides a light weight implementation of the standard distribution functions for the inverse gamma distribution, wrapping those for the gamma distribution in the stats package.
This package provides a command line parser to be used with Rscript to write shebang scripts that gracefully accept positional and optional arguments and automatically generate usage notices.
In Shiny apps, it is sometimes useful to store information on a particular item in a tooltip. Prompter allows you to easily create such tooltips, using Hint.css.
This package lets you compute case-wise and cluster-wise derivative for mixed effects models with respect to fixed effects parameter, random effect (co)variances, and residual variance.
This package provides an implementation of bee swarm plots. The bee swarm plot is a one-dimensional scatter plot like stripchart, but with closely-packed, non-overlapping points.
Read large text files by splitting them in smaller files. This package also provides some convenient wrappers around fread() and fwrite() from package data.table.
This package allows you to install specified versions of R packages hosted on CRAN and provides functions to list available versions and the versions of currently installed packages.
Excon was designed to be simple, fast and performant. It works great as a general HTTP(s) client and is particularly well suited to usage in API clients.
Guard is a command line tool to easily handle events on file system modifications. Guard automates various tasks by running custom rules whenever file or directories are modified.
Use hail via basilisk when appropriate, or via reticulate. This package can be used in terra.bio to interact with UK Biobank resources processed by hail.is.
This package is a wrapper of Integrative Genomics Viewer (IGV). It comprises an htmlwidget version of IGV. It can be used as a module in Shiny apps.
This is a collection of utility functions that allow to perform exploration of and calculations to RNA sequencing data, in a modular, pipe-friendly and tidy fashion.
Get a current financial year, start of current month, End of current month, start of financial year and end of it. Allow for offset from the date.
Method to implement some newly developed methods for the estimation of the conditional survival function. See Meira-Machado, Sestelo and Goncalves (2016) <doi:10.1002/bimj.201500038>.
Encode and decode c-squares, from and to simple feature (sf) or spatiotemporal arrays (stars) objects. Use c-squares codes to quickly join or query spatial data.
Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) for clustered data documented in Jiang et. al (2020) <doi:10.18637/jss.v096.i06>.
Estimation, testing and regression modeling of subdistribution functions in competing risks using quantile regressions, as described in Peng and Fine (2009) <DOI:10.1198/jasa.2009.tm08228>.
This package provides a tool for manipulating data using the generic formula. A single formula allows to easily add, replace and remove variables before running the analysis.