KEGGgraph - KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.
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pathwaysgraphandnetworkvisualizationkegg
9.44 score 24 dependents 200 scripts 9.7k downloadsBioQC - Detect tissue heterogeneity in expression profiles with gene sets
BioQC performs quality control of high-throughput expression data based on tissue gene signatures. It can detect tissue heterogeneity in gene expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is optimised for high performance.
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geneexpressionqualitycontrolstatisticalmethodgenesetenrichmentcpp
7.70 score 5 stars 1 dependents 1 scripts 625 downloadsribiosUtils - 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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5.98 score 1 stars 8 dependents 79 scripts 278 downloadsribiosArg - 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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4.96 score 3 dependents 41 scripts 202 downloadsribiosIO - 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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4.92 score 3 dependents 31 scripts 217 downloadsribiosPlot - 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>.
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4.86 score 1 stars 3 dependents 32 scripts 197 downloadsRTCA - Open-source toolkit to analyse data from xCELLigence System (RTCA)
Import, analyze and visualize data from Roche(R) xCELLigence RTCA systems. The package imports real-time cell electrical impedance data into R. As an alternative to commercial software shipped along the system, the Bioconductor package RTCA provides several unique transformation (normalization) strategies and various visualization tools.
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immunooncologycellbasedassaysinfrastructurevisualizationtimecourse
4.64 score 11 scripts 516 downloadsddCt - The ddCt Algorithm for the Analysis of Quantitative Real-Time PCR (qRT-PCR)
The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.
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geneexpressiondifferentialexpressionmicrotitreplateassayqpcr
4.38 score 9 scripts 607 downloadsribiosNGS - 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
4.28 score 2 stars 1 dependents 16 scriptsribiosExpression - 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
4.16 score 2 dependents 16 scriptsribiosGSEA - 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
3.75 score 2 stars 14 scriptsribiosGraph - 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>.
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3.48 score 195 downloadsribiosAnnotation - 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.
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3.12 score 3 dependents 29 scripts