Data frames with time information are subset and flagged with period information. Data frames with times are dealt as timeDF objects and periods are represented as periodDF objects.

Species trait data from many sources, including sequence data from NCBI (<https://www.ncbi.nlm.nih.gov/>), plant traits from BETYdb, and data from EOL Traitbank and BirdLife International.

R package accompanying the book Working with dynamic models for agriculture and environment, by Daniel Wallach (INRAE), David Makowski (INRAE), James W. Jones (U.of Florida), Francois Brun (ACTA), 2019.

The main purpose of this package is to perform simulation-based estimation of stochastic actor-oriented models for longitudinal network data collected as panel data. Dependent variables can be single or multivariate networks, which can be directed, non-directed, or two-mode; and associated actor variables. There are also functions for testing parameters and checking goodness of fit. An overview of these models is given in Snijders (2017), <doi:10.1146/annurev-statistics-060116-054035>.

This package provides a simplified version of the Portal Project Database designed for teaching. It provides a real world example of life-history, population, and ecological data, with sufficient complexity to teach many aspects of data analysis and management, but with many complexities removed to allow students to focus on the core ideas and skills being taught. The full database (which should be used for research) is available at <https://github.com/weecology/PortalData>.

For any two way feature-set from a pair of pre-processed omics data, 3 different true discovery proportions (TDP), namely pairwise-TDP, column-TDP and row-TDP are calculated. Due to embedded closed testing procedure, the choice of feature-sets can be changed infinite times and even after seeing the data without any change in type I error rate. For more details refer to Ebrahimpoor et al., (2024) <doi:10.48550/arXiv.2410.19523>.

Network-based regularization has achieved success in variable selection for high-dimensional biological data due to its ability to incorporate correlations among genomic features. This package provides procedures of network-based variable selection for generalized linear models (Ren et al. (2017) <doi:10.1186/s12863-017-0495-5> and Ren et al.(2019) <doi:10.1002/gepi.22194>). Continuous, binary, and survival response are supported. Robust network-based methods are available for continuous and survival responses.

Interface to the ChEA3 transcription factor enrichment API. ChEA3 integrates evidence from ChIP-seq, co-expression, and literature resources to prioritize transcription factors regulating a given set of genes. This package provides convenient R functions to query the API, retrieve ranked results across collections (including integrated scores), and standardize output for downstream analysis in R/Bioconductor workflows. See <https://maayanlab.cloud/chea3/> or Keenan (2019) <doi:10.1093/nar/gkz446> for further details.

This package extends the ggplot2 plotting system which implements a grammar of graphics. ggtree is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.

This package implements infrastructures for ontology analysis by offering efficient data structures, fast ontology traversal methods, and elegant visualizations. It provides a robust toolbox supporting over 70 methods for semantic similarity analysis.

This package provides functions to estimate variance-mean dependence in count data from high-throughput nucleotide sequencing assays and test for differential expression based on a model using the negative binomial distribution.

This package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site.

This package conducts batch effects removal from a taxa read count table by a conditional quantile regression method. The distributional attributes of microbiome data - zero-inflation and over-dispersion, are simultaneously considered.

This package provides an infrastructure for representing, manipulating and analyzing transaction data and patterns (frequent itemsets and association rules). It also provides C implementations of the association mining algorithms Apriori and Eclat.

This package provides key-value stores with automatic pruning. Caches can limit either their total size or the age of the oldest object (or both), automatically pruning objects to maintain the constraints.

RESTinio is a header-only C++14 library that gives you an embedded HTTP/Websocket server. It is based on standalone version of ASIO and targeted primarily for asynchronous processing of HTTP-requests.

ruby-unf is a wrapper library to bring Unicode Normalization Form support to both Ruby and JRuby. It uses unf_ext on CRuby and java.text.Normalizer on JRuby.

Spy is a mocking library. By default, it will raise an error if you attempt to stub a method that doesn't exist or call the stubbed method with the wrong arity.

This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.

This package provides tools and functions to efficiently create datasets used in pharmacometric analysis. Additional functionality is added to create documentation and prepare files for submission and quality control purposes.

This package provides a collection of functions that allow servers (specifically BPKP) to summarize and verify shift earnings, identify composition of tips and hourly wage, and track performance through several metrics.

This includes functions for creating 3D and 4D images using WebGL', rgl', and JavaScript commands. This package relies on the X toolkit ('XTK', <https://github.com/xtk/X#readme>).

An umbrella package providing a phenotype/genotype data structure and scalable and efficient computational methods for large genomic datasets in combination with several other packages: BEDMatrix', LinkedMatrix', and symDMatrix'.

Can take in images in either .jpg, .jpeg, or .png format and creates a colour palette of the most frequent colours used in the image. Also provides some custom colour palettes.