Bioconductor Topics

Integrate microRNA and gene expression to decipher pathway complexity

Mean Log P Analysis

Multi Omics Survival Clip

MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis

Bayesian clustering and imputationa of single cell methylomes

Network-based prioritization of putative metabolite IDs

Metabolite Mashing with R

Single cell replicability analysis

Metabolic Pathway Analysis of RNA

METabolomics pre-PRocessing, functiOnal analysis and VIZualisation

MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways

Identify oncogenes and tumor suppressor genes from omics data

Identify oncogenes and tumor suppressor genes from omics data

An R package for integrated analysis of temporal RNA-seq data with multiple biological conditions

Pathways from the NCI Pathways Database

Compute gene set scores from a deep learning framework

NetPathMiner for Biological Network Construction, Path Mining and Visualization

NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment

R wrapper for the OMA REST API

OmniPath web service client and more

Pathway Association Study Tool (PAST)

Phenotype Consensus ANalysis (PCAN)

Inferring functionally related proteins using protein interaction networks

Detection of miRNAs that regulate interacting groups of pathways

Prediction of pathway-related protein-protein interaction networks

An R package for pathway analysis using topological information

PhenoGeneRanker: A gene and phenotype prioritization tool

RNA Centric Annotation System

R package implementing the Cytoscape Exchange (CX) format

Molecular Informatics Toolkit for Compound-Protein Interaction in Drug Discovery

Client for the Reactome Analysis Service for comparative multi-omics gene set analysis

Reactome Pathway Analysis

Investigating regions of interest and performing regional cell type-specific analysis with spatial transcriptomics data

Tools for making reports in various formats

"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

SBML-R Interface and Analysis Tools

Predicting cell states and their variability in single-cell or spatial omics data

Information Accretion-based Function Predictor Evaluation

Surface Protein Prediction and Identification

TCGAbiolinks: An R/Bioconductor package for integrative analysis with GDC data

Tools for Molecular Signatures

R Interface to UniProt Web Services

Quantification and Visualization of Variations of Splicing in Population

ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and semantic similarity

Annotation-Based Analysis of Specific Interactions

Annotation tools for Affymetrix biological metadata

Annotation for microarrays

Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor Landscape

Interactive Multi-Omics Cancers Data Visualization and Analysis

Biodb, a Library and a Development Framework for Connecting to Chemical and Biological Databases