Bioconductor Packages

Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

High-performing routines for the randomization of a bipartite graph (or a binary event matrix), undirected and directed signed graph preserving degree distribution (or marginal totals)

BioCarta Pathway Images

Functional Similarities

Bioinformatics Genetic Algorithm (BioGA)

Model-View-Controller (MVC) Classes That Use Biobase

Biological Network Analysis in R

Biological Network Reconstruction Omnibus

Routines for the functional analysis of biological networks

Write, containerize, publish and version Quarto books with Bioconductor

An interactive Shiny dashboard for Bioconductor package maintainers

Representing Different Biological Sets

Tools to aid the development of Bioconductor Workflow packages

Efficient manipulation of biological strings

This R package for performing module repertoire analyses and generating fingerprint representations

Cohort-aware methods for intrinsic molecular subtyping of breast cancer

Code for using BridgeDb identifier mapping framework from within R

BrowserViz: interactive R/browser graphics using websockets and JSON

Infer Ligand-Receptor Interactions from bulk expression (transcriptomics/proteomics) data, or spatial transcriptomics

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Spatially Informed Cell Type Deconvolution for Spatial Transcriptomics

A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

Cytometry dATa anALYSis Tools

CBN2Path: an R/Bioconductor package for the analysis of cancer progression pathways using Conjunctive Bayesian Networks

plot bayesian network inferred from gene expression data based on enrichment analysis results

Case Control Allele Frequency Estimation

Plots For Visualising Cell-Cell Interactions

Clustering Deviation Index (CDI)

Co-expression Modules identification Tool

An R package for analysis of case-control studies in genetic epidemiology

Normalization of array CGH data with imbalanced aberrations.

Dimension Reduction for Array CGH Data with Minimal Information Loss.

CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis

A normalization method for Copy Number Aberration in cancer samples

CNE Detection and Visualization

Addon to CellNOptR: Fuzzy Logic

Reliable CNV detection in targeted sequencing applications

Identifies false positives of CNV calling tools by using SNV calls

Copy Number Visualization

A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing

Data normalization by matrix raking

CPSM: Cancer patient survival model

Shiny Application for Interactive CRISPR Screen Visualization, Exploration, Comparison, and Filtering

Chip-seq Signal Quantifier Pipeline

Package for CTDbase data query, visualization and downstream analysis

An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations

Calibration curves for targeted proteomics, lipidomics and metabolomics data

A mass spectrometry imaging toolbox for statistical analysis

Category Analysis