Bioconductor Topics

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Adaptive Dropout Imputer (ADImpute)

Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach

Affinity Network Fusion for Complex Patient Clustering

visualization and annotation of isotopic enrichment patterns of peptides and metabolites with stable isotope labeling from proteomics and metabolomics

Automated spectraL Processing System for NMR

Assess Gene Predictions Using Proteomics and Evolutionary Conservation

BANDITS: Bayesian ANalysis of DIfferenTial Splicing

Refitting diploid region profiles using a clustering procedure

Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

Batch Effects Quality Control Software

BayesKnockdown: Posterior Probabilities for Edges from Knockdown Data

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

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

An interactive Shiny dashboard for Bioconductor package maintainers

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

Cohort-aware methods for intrinsic molecular subtyping of breast cancer

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

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

Plots For Visualising Cell-Cell Interactions

Clustering Deviation Index (CDI)

Co-expression Modules identification Tool

Dimension Reduction for Array CGH Data with Minimal Information Loss.

CNE Detection and Visualization

Addon to CellNOptR: Fuzzy Logic

Identifies false positives of CNV calling tools by using SNV calls

Copy Number Visualization

CPSM: Cancer patient survival model

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

Package for CTDbase data query, visualization and downstream analysis

Calibration curves for targeted proteomics, lipidomics and metabolomics data

Causal network analysis methods

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

ChIPexoQual

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization

R interface to a subset of OpenBabel functionalities

Cheminformatics Toolkit for R

Heat map plotting by genome coordinate