recoup

Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.

A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.

This package performs differential pattern analysis for Ribo-seq data. It identifies genes with significantly different patterns in the ribosome footprint between two conditions. RiboDiPA contains five major components including bam file processing, P-site mapping, data binning, differential pattern analysis and footprint visualization.

systemPipeR is a workflow management environment for reproducible data analysis that integrates R with command-line software. It enables researchers to design, execute, and report complex workflows on local machines and HPC systems. The framework combines R-based analysis with external tools through a Common Workflow Language (CWL) interface, manages workflow dependencies and restart capabilities, and automatically generates reproducible scientific analysis reports. The companion package systemPipeRdata provides ready-to-use workflow templates that simplify workflow setup and customization. Alternatively, workflow templates can be loaded from dedicated GitHub repositories.

This package performs degradation normalization in bulk RNA-seq data to improve differential expression analysis accuracy. It provides estimates for each gene within each sample.

Provides some legacy utility functions for performing single-cell analyses. Most of these functions are deprecated in favor of newer, more performant alternatives. We just keep this package around for back-compatibility and to point to the replacement functions.