This is a small package to provide consistent tick marks for plotting ggplot2 figures. It provides breaks and labels for ggplot2 without requiring ggplot2 to be installed.

Create plots and tables in a consistent style with WaSHI (Washington Soil Health Initiative) branding. Use washi to easily style your ggplot2 plots and flextable tables.

This package provides an Interface to Zenodo (<https://zenodo.org>) REST API, including management of depositions, attribution of DOIs by Zenodo and upload and download of files.

Tool-set to support Bayesian evidence synthesis. This includes meta-analysis, (robust) prior derivation from historical data, operating characteristics and analysis (1 and 2 sample cases). Please refer to Weber et al. (2021) <doi:10.18637/jss.v100.i19> for details on applying this package while Neuenschwander et al. (2010) <doi:10.1177/1740774509356002> and Schmidli et al. (2014) <doi:10.1111/biom.12242> explain details on the methodology.

This package implements a series of robust Kalman filtering approaches. It implements the additive outlier robust filters of Ruckdeschel et al. (2014) <arXiv:1204.3358> and Agamennoni et al. (2018) <doi:10.1109/ICRA.2011.5979605>, the innovative outlier robust filter of Ruckdeschel et al. (2014) <arXiv:1204.3358>, as well as the innovative and additive outlier robust filter of Fisch et al. (2020) <arXiv:2007.03238>.

The main purpose of this package is to streamline the generation of exams that include random elements in exercises. Exercises can be defined in a table, based on text and figures, and may contain gaps to be filled with provided options. Exam documents can be generated in various formats. It allows us to generate a version for conducting the assessment and another version that facilitates correction, linked through a code.

This is a package to perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113).

This package provides syntax highlighting for R source code. Currently it supports LaTeX and HTML output. Source code of other languages is supported via Andre Simon's highlight package.

This package provides an R interface to HiGHS, an optimization solver. It is designed for solving mixed-integer optimization problems with quadratic or linear objectives and linear constraints.

Servr provides an HTTP server in R to serve static files, or dynamic documents that can be converted to HTML files (e.g., R Markdown) under a given directory.

ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.

Perform non-parametric analysis of response curves as described by Childs, Bach, Franken et al. (2019): Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins.

Detection of ligand-protein interactions from 2D thermal profiles (DLPTP), Performs an FDR-controlled analysis of 2D-TPP experiments by functional analysis of dose-response curves across temperatures.

This package is devoted to analyzing MeRIP-seq data. Current functionalities include 1. detect transcriptome wide m6A methylation regions 2. detect transcriptome wide differential m6A methylation regions.

This package provides a system to build, visualise and evaluate Bayesian belief networks. The methods are described in Stafford et al. (2015) <doi:10.12688/f1000research.5981.1>.

Functions, data and code for Hilbe, J.M. 2011. Negative Binomial Regression, 2nd Edition (Cambridge University Press) and Hilbe, J.M. 2014. Modeling Count Data (Cambridge University Press).

An efficient and convenient set of functions to perform differential network estimation through the use of alternating direction method of multipliers optimization with a variety of loss functions.

This package provides methods and utilities for causal emergence. Used to explore and compute various information theory metrics for networks, such as effective information, effectiveness and causal emergence.

Simultaneous modeling of the quantile and the expected shortfall of a response variable given a set of covariates, see Dimitriadis and Bayer (2019) <doi:10.1214/19-EJS1560>.

An R client for the Federal Reserve Economic Data ('FRED') API <https://research.stlouisfed.org/docs/api/>. Functions to retrieve economic time series and other data from FRED'.

Does family-based gene by environment interaction tests, joint gene, gene-environment interaction test, and a test of a set of genes conditional on another set of genes.

This package provides functions for performing graphical difference testing. Differences are generated between raster images. Comparisons can be performed between different package versions and between different R versions.

This package creates plots of peptides from shotgun proteomics analysis of secretome and lysate samples. These plots contain associated protein features and scores for potential secretion and truncation.

Automated analysis and modeling of longitudinal omics data (e.g. breath metabolomics') using generalized spline mixed effect models. Including automated filtering of noise parameters and determination of breakpoints.