Reconstructing Interlog Protein Network (IPN) integrated from several Protein protein Interaction Networks (PPINs). Using this package, overlaying different PPINs to mine conserved common networks between diverse species will be applicable.

The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites. This package is an R wrapper of the lastest MACS3.

The aim of oppti is to analyze protein (and phosphosite) expressions to find outlying markers for each sample in the given cohort(s) for the discovery of personalized actionable targets.

Runitor runs the supplied command, captures its output, and based on its exit code reports successful or failed execution to https://healthchecks.io or your private instance.

Milo performs single-cell differential abundance testing. Cell states are modelled as representative neighbourhoods on a nearest neighbour graph. Hypothesis testing is performed using a negative bionomial generalized linear model.

ASICS quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty.

This package provides the ASCAT R package that can be used to infer tumour purity, ploidy and allele-specific copy number profiles.

This package provides the header files for a stripped-down version of the plog header-only C++ logging library, and a method to log to R's standard error stream.

How fast can you type R functions on your keyboard? Find out by running a zty.pe game: export R functions as instructions to type to destroy opponents' vessels.

This is a package for simplified document database access and manipulation, providing a common API across supported NoSQL databases Elasticsearch, CouchDB, MongoDB as well as SQLite/JSON1, PostgreSQL, and DuckDB.

This package provides two high quality and fast PPRNGs that may be used in an OpenMP parallel environment. In addition, there is a generator for one dimensional low-discrepancy sequence.

This package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

An approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for 210Pb-dated deposits using prior information. It can combine 210Pb, radiocarbon, and other dates in the chronologies. See Aquino et al. (2018) <doi:10.1007/s13253-018-0328-7>. Note that parts of the code underlying rplum are derived from the rbacon package by the same authors, and there remains a degree of overlap between the two packages.

This package implements specialized algorithms that enable genetic ancestry inference from various cancer sequences sources (RNA, Exome and Whole-Genome sequences). This package also implements a simulation algorithm that generates synthetic cancer-derived data. This code and analysis pipeline was designed and developed for the following publication: Belleau, P et al. Genetic Ancestry Inference from Cancer-Derived Molecular Data across Genomic and Transcriptomic Platforms. Cancer Res 1 January 2023; 83 (1): 49–58.

This package provides tools to read, write, parse, and analyze forest fire history data (e.g. FHX). Described in Malevich et al. (2018) <doi:10.1016/j.dendro.2018.02.005>.

This package provides a wrapper for the CDRC API that returns data frames or sf of CDRC data. The API web reference is:<https://api.cdrc.ac.uk/swagger/index.html>.

Covariate-augumented generalized factor model is designed to account for cross-modal heterogeneity, capture nonlinear dependencies among the data, incorporate additional information, and provide excellent interpretability while maintaining high computational efficiency.

This package implements double hierarchical generalized linear models in which the mean, dispersion parameters for variance of random effects, and residual variance (overdispersion) can be further modeled as random-effect models.

This package provides R access to election results data. Wraps elex (https://github.com/newsdev/elex/), a Python package and command line tool for fetching and parsing Associated Press election results.

Sparse large Directed Acyclic Graphs learning with a combination of a convex program and a tailored genetic algorithm (see Champion et al. (2017) <https://hal.archives-ouvertes.fr/hal-01172745v2/document>).

This package provides functionality to download and cache files from Hugging Face Hub <https://huggingface.co/models>. Uses the same caching structure so files can be shared between different client libraries.

H3 is a hexagonal hierarchical spatial index developed by Uber <https://h3geo.org/>. This package exposes the source code of H3 (written in C') to routines that are callable through R'.

This package contains functions for fitting hierarchical versions of EVSD, UVSD, DPSD, DPSD with d restricted to be positive, and our gamma signal detection model to recognition memory confidence-ratings data.

This package provides tools for estimation and inference of conditional densities, derivatives and functions. This is the companion software for Cattaneo, Chandak, Jansson and Ma (2024) <doi:10.3150/23-BEJ1711>.