This package provides functions and data sets for data sharpening. Nonparametric regressions are computed subject to smoothness and other kinds of penalties.

Streamlined workflow from deconvolution of bulk RNA-seq data to downstream differential expression and gene-set enrichment analysis. Provide various visualization functions.

An efficient algorithm for data twinning. This work is supported by U.S. National Science Foundation grants DMREF-1921873 and CMMI-1921646.

This package provides the "r, q, p, and d" distribution functions for the triangle distribution. Also includes maximum likelihood estimation of parameters.

This package provides a Python interface structured according to the general form described in package XR and in the book "Extending R".

This package implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.

Boosting supported network analysis for high-dimensional omics applications. This package comes bundled with the MC-UPGMA clustering package by Yaniv Loewenstein.

This package provides example datasets that represent 'real world examples' of Affymetrix data, unlike the artificial examples included in the package affy.

This package computes differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.

This package provides useful functions to deal with the haven_labelled and haven_labelled_spss classes introduced by the haven package.

This package provides a %dopar% adapter such that any type of futures can be used as backends for the foreach framework.

This package extends the ggplot2 plotting system to support network visualization. Inspired by ggtree, ggtangle is designed to work with network associated data.

This package provides tools to integrate nucleotide sequencing data (variant call format, e.g. VCF or BCF) or meta-analysis results in R.

BRASS (Bare-Metal Ruby Assertion System Standard) is a basic foundational assertions framework for other assertion and test frameworks to make use of.

Mocha is a mocking and stubbing library with JMock/SchMock syntax, which allows mocking and stubbing of methods on real (non-mock) classes.

Fast alternatives to several relatively slow raster package functions. For large rasters, the functions run from 5 to approximately 100 times faster than the raster package functions they replace. The fasterize package, on which one function in this package depends, includes an implementation of the scan line algorithm attributed to Wylie et al. (1967) <doi:10.1145/1465611.1465619>.

Read Statistical Data and Metadata Exchange (SDMX) XML data. This the main transmission format used in official statistics. Data can be imported from local SDMX-ML files or a SDMX web-service and will be read in as is into a dataframe object. The RapidXML C++ library <https://rapidxml.sourceforge.net/> is used to parse the XML data.

An R interface to United States Environmental Protection Agency (EPA) Assessment, Total Maximum Daily Load (TMDL) Tracking and Implementation System ('ATTAINS') data. ATTAINS is the EPA database used to track information provided by states about water quality assessments conducted under federal Clean Water Act requirements. ATTAINS information and API information is available at <https://www.epa.gov/waterdata/attains>.

An interface to iDigBio's search API that allows downloading specimen records. Searches are returned as a data.frame. Other functions such as the metadata end points return lists of information. iDigBio is a US project focused on digitizing and serving museum specimen collections on the web. See <https://www.idigbio.org> for information on iDigBio.

The package provides the data for the RDP Classifier 2.14 released in August 2023. It contains the latest bacterial and archaeal taxonomy training set No. 19 as described in Wang Q, Cole JR. 2024. Updated RDP taxonomy and RDP Classifier for more accurate taxonomic classification. Microbiol Resour Announc 0:e01063-23. <doi.org/10.1128/mra.01063-23>.

The TRUST4 or MiXCR is used to identify the clonotypes. The goal of rTCRBCRr is to process the results from these clonotyping tools, and analyze the clonotype repertoire metrics based on chain names and IGH isotypes. The manuscript is still under preparation for publication for now. The references describing the methods in this package will be added later.

This package provides functions to process minute level actigraphy-measured activity counts data and extract commonly used physical activity volume and fragmentation metrics.

This package provides a lightweight package to access spatial basemaps from open sources such as OpenStreetMap', Carto', Mapbox and others in R.

Calculations of "EP15-A3 document. A manual for user verification of precision and estimation of bias" CLSI (2014, ISBN:1-56238-966-1).