This package infers directional Conservative causal core (gene) networks (C3NET). This is a version of the algorithm C3NET with directional network.

The package contains functions for inferece of target gene regulation by miRNA, based on only target gene expression profile.

The rfacts package is an R interface to the Fixed and Adaptive Clinical Trial Simulator FACTS. It programmatically invokes FACTS to run clinical trial simulations. It aggregates simulation output data into tidy data frames. These capabilities provide end-to-end automation for large-scale simulation pipelines, and they enhance computational reproducibility.

This package provides an R wrapper to the Python natural language processing (NLP) library spaCy, from http://spacy.io.

This package provides an R tool for estimating and partitioning R2 in generalized linear mixed models (GLMMs) based on predictor variance.

This package provides empirical likelihood ratio tests for means/quantiles/hazards from possibly censored and/or truncated data. It also does regression.

This package provides a series of additional Tcl commands and Tk widgets with style and various functions to supplement the tcltk package

Contains functions for data preparation, descriptives, hazard estimation and prediction with Aalen-Johansen or simulation in competing risks and multi-state models.

This package provides an R interface to the jExcel library to create web-based interactive tables and spreadsheets compatible with spreadsheet software.

This package provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.

This package provides graphical scales that map data to aesthetics, and provides methods for automatically determining breaks and labels for axes and legends.

This package provides binning and plotting functions for hexagonal bins. It uses and relies on grid graphics and formal (S4) classes and methods.

This package provides a pillar generic designed for formatting columns of data using the full range of colours provided by modern terminals.

This package provides procedures to create preliminary exploratory data visualisations of an entire dataset to identify problems or unexpected features using ggplot2.

This package implements different robust clustering algorithms (tclust) based on trimming and including some graphical diagnostic tools (ctlcurves and DiscrFact).

RSVSim is a package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.

Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends the monocle package for use in chromatin accessibility data.

This package contains class definitions for two-color spotted microarray data. It also includes functions for data input, diagnostic plots, normalization and quality checking.

This package is a compatibility wrapper to replace the orphaned package by Romain Francois. New applications should use the openssl or base64enc package instead.

This package provides tools to fit a variety of latent variable models, including confirmatory factor analysis, structural equation modeling and latent growth curve models.

The SeqSQC is designed to identify problematic samples in NGS data, including samples with gender mismatch, contamination, cryptic relatedness, and population outlier.

LLD is a high-performance linker, built as a set of reusable components which highly leverage existing libraries in the larger LLVM Project.

This package provides functions for manipulation of R documentation objects, including functions reprompt() and ereprompt() for updating Rd documentation for functions, methods and classes; it also includes Rd macros for citations and import of references from bibtex files for use in Rd files and roxygen2 comments, as well as many functions for manipulation of references and Rd files.

This package provides a collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control.