Bioconductor Packages

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.

Fast and accurate scRNA-seq cell type identification

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

CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution

Synthesis of microarray-based classification

A normalization method for Copy Number Aberration in cancer samples

Add-on to CellNOptR: Discretized time treatments

ODE add-on to CellNOptR

Convert segment data into a region by sample matrix to allow for other high level computational analyses.

Reliable CNV detection in targeted sequencing applications

Summarization and expression/phenotype association of CNV ranges

Identifies false positives of CNV calling tools by using SNV calls

Copy Number Visualization

CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.

Coordinate Covariation Analysis

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

Combinatorial Polyfunctionality Analysis of Single Cells

Data normalization by matrix raking

Cost Sensitive Network for node label prediction on graphs with highly unbalanced labelings

COexpression Tables ANalysis

CPSM: Cancer patient survival model

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

Design of guide RNAs in CRISPR genome-editing systems

CRImage a package to classify cells and calculate tumour cellularity

Statistical tools for the analysis of ChIP-seq data

Calculate per-cell gene signature scores in scRNA-seq data using cell set overlaps

Chip-seq Signal Quantifier Pipeline

Identification of cell-type-specific spatially variable genes accounting for excess zeros

Data companion to CTexploreR

Explores Cancer Testis Genes

Candidate Driver Analysis

Calibration curves for targeted proteomics, lipidomics and metabolomics data

A mass spectrometry imaging toolbox for statistical analysis

Read and write mass spectrometry imaging files

This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters

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

Predict genes expressed selectively in specific cell types

Supervised Non-negative Matrix Factorization for Dimensional Reduction in Single-Cell Analysis

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

Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Cepo for the identification of differentially stable genes

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates