designit - Blocking and Randomization for Experimental Design

Intelligently assign samples to batches in order to reduce batch effects. Batch effects can have a significant impact on data analysis, especially when the assignment of samples to batches coincides with the contrast groups being studied. By defining a batch container and a scoring function that reflects the contrasts, this package allows users to assign samples in a way that minimizes the potential impact of batch effects on the comparison of interest. Among other functionality, we provide an implementation for OSAT score by Yan et al. (2012, <doi:10.1186/1471-2164-13-689>).

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design-of-experimentsrandomization

6.68 score 8 stars 30 scripts 632 downloads

ribiosUtils - Utilities from and Interface to the 'Bioinfo-C' ('BIOS') Library

Provides interface to the 'Bioinfo-C' (internal name: 'BIOS') library and utilities. 'ribiosUtils' is a Swiss-knife for computational biology in drug discovery, providing functions and utilities with minimal external dependency and maximal efficiency.

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5.84 score 1 stars 8 dependents 72 scripts 240 downloads

ribiosIO - Input/Output Utilities of the 'ribios' Suite

Provides data structures and functions for file input/output in the 'ribios' software suite, supporting common bioinformatics and computational biology file formats, designed for fast loading and high performance with minimal dependencies.

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4.95 score 3 dependents 33 scripts 142 downloads

Vennerable - Venn and Euler area-proportional diagrams

A package for drawing various species of Venn diagrams.

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4.94 score 349 scripts

ribiosArg - Argument Handling for Command-Line, Stand-Alone R Scripts

Provides functions to handle command-line arguments for R scripting. It enables building stand-alone R programs that accept and parse command-line options in 'BIOS' style. Zhang (2025) <https://github.com/bedapub/ribiosArg>.

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4.88 score 3 dependents 34 scripts 126 downloads

ribiosPlot - Plotting Module of the 'ribios' Software Suite

Provides data structures and functions for data transformation and visualization in computational biology in drug discovery as part of the 'ribios' software suite. Zhang (2025) <https://github.com/bedapub/ribiosPlot>.

Last updated

4.86 score 1 stars 3 dependents 32 scripts 145 downloads

ribiosNGS - Differential gene expression analysis for next-generation sequencing data in the 'ribios' suite

Provides a comprehensive workflow for differential gene expression analysis of RNA-seq data using 'edgeR' and 'limma'-voom pipelines. The package supports count filtering, normalization, surrogate variable analysis, batch correction, and visualization including volcano plots, smear plots, and PCA. It integrates with the 'ribios' suite of packages and is designed for reproducible bioinformatics analyses.

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differentialexpressiongeneexpressionrnaseqtranscriptomics

4.43 score 2 stars 1 dependents 15 scripts

ribiosExpression - Data Structures and Utilities for Gene Expression Analysis

Provides data structures and utility functions for gene expression analysis. It includes the DesignContrast class for representing study designs and contrasts used in differential expression analysis, functions for importing and exporting expression data in GCT/CLS formats, tools for probeset summarization and filtering, and interfaces to limma-based differential gene expression workflows. The package works with Biobase ExpressionSet objects and integrates with the limma framework.

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geneexpressiondifferentialexpressionmicroarraydataimportvisualization

3.98 score 2 dependents 16 scripts

ribiosMath - Mathematical and Statistical Tools in 'ribios'

Mathematical and statistical tools for computational biology in drug discovery. Functions are designed for high performance. Zhang (2025) <https://github.com/bedapub/ribiosMath>.

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openblascpp

3.78 score 8 scripts 111 downloads

ribiosGSEA - Gene-Set Enrichment Analysis Tools in 'ribios'

Provides data structure and functions for gene-set analysis and post-processing of analysis results.

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cppopenmp

3.48 score 2 stars 6 scripts

ribiosGraph - Manipulate and Visualize Graphs in the 'ribios' Software Suite

Tools to manipulate and visualize graphs (networks) for computational biology in drug discovery, for instance functions for creating bipartite graphs and for interactive visualizations. Zhang (2025) <https://github.com/bedapub/ribiosGraph>.

Last updated

3.48 score 145 downloads

ribiosAnnotation - Annotation of Genes, RNAs, and Proteins in 'ribios'

Retrieves annotation information of genomic features including genes, RNAs, and proteins from databases. It supports querying by gene identifiers, gene symbols, UniProt accessions, Ensembl identifiers, and RefSeq identifiers, as well as mapping orthologs across species using NCBI data.

Last updated

3.40 score 3 dependents 28 scripts