Bioconductor Packages

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

BrowserVizDemo: How to subclass BrowserViz

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

CAncer bioMarker Prediction Pipeline 2 (CAMPP2)

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

Carbon Tetrachloride (CCl4) treated hepatocytes

Clustering Deviation Index (CDI)

Co-expression Modules identification Tool

Hub package for the precomputed data of CENTRE and example data

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.

Chaos Game Representation for Phylogenetic Analysis

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

"CITEViz: Classifying Cell Clusters in CITE-Seq Data using the Flow Cytometry Gating Workflow"

Peripheral blood CITE-Seq dataset with 10K cells for use with CITEViz tutorial

Curated Latent-variable Analysis with Molecular Priors

Experiment data for CLAMP package

A Package for CLL Gene Expression Data

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

A Framework of Functions to Combine, Analize and Interpret CNVs Calling Results

Copy Number Visualization

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

Annotations for City of Hope CpG Island Analysis Pipeline

Data normalization by matrix raking

Data to support sexually dimorphic and COPD differential analysis for gene expression and methylation.

COSMIC.67

CPSM: Cancer patient survival model

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

ChIP-Seq Statistical Power

Chip-seq Signal Quantifier Pipeline

CTDPathSim: Cell line-tumor deconvoluted pathway-based similarity in the context of precision medicine in cancer

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

Cancer subtypes identification, validation and visualization based on multiple genomic data sets