Bioconductor Packages

A matrix data storage object held in temporary files

Microarray Data related methods that utlize BufferedMatrix objects

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

Bumpy Matrix of Non-Scalar Objects

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

CGHbase: Base functions and classes for arrayCGH data analysis.

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

COexpression Tables ANalysis

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

Data companion to CTexploreR

Explores Cancer Testis Genes

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

Read and write mass spectrometry imaging files

Category Analysis

Causal network analysis methods

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

Cellular DNA Barcode Analysis toolkit

Construct Benchmarks for Single Cell Analysis Methods

Evaluate Cellspecific Mixing

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

Reconstruction, visualization and analysis of branching trajectories

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Quantitative comparison of multiple ChIP-seq datasets

Quality metrics for ChIPseq data