Bioconductor Packages

ODE add-on to CellNOptR

Reliable CNV detection in targeted sequencing applications

Identifies false positives of CNV calling tools by using SNV calls

Coordinate Covariation Analysis

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

CRImage a package to classify cells and calculate tumour cellularity

Genomic coordinates of CTCF binding sites, with orientation

Package for CTDbase data query, visualization and downstream analysis

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

Construct Benchmarks for Single Cell Analysis Methods

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

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

Quantitative comparison of multiple ChIP-seq datasets

Identifying Protein Binding Sites in High-Throughput Sequencing Data

Simulation of ChIP-seq experiments

R interface to a subset of OpenBabel functionalities

Cheminformatics Toolkit for R

Analysis of single-cell epigenomics datasets with a Shiny App

Infrastructure for Chromatographic Mass Spectrometry Data

A framework for cross-validated classification problems, with applications to differential variability and differential distribution testing

Infers clonal composition of a tumor

Simulation of Tumor Clonal Evolution with Realistic Sequencing Noise

Clustering of MS2 Spectra for Metabolite Identification

ClustAll: Data driven strategy to robustly identify stratification of patients within complex diseases

Clustering of Immune Receptor Repertoires

Calculate similarity of clusters from different single cell samples using foldchanges

Judging Quality of Clustering Methods using Mutual Information

The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data

Coordinated Gene Activity in Pattern Sets

An Investigation Across Different Species and Tissues

ConsensusClusterPlus

Create Copy-Number Plots using karyoploteR functionality

Helper files for CopywriteR

Coralysis sensitive identification of imbalanced cell types and states in single-cell data via multi-level integration

Classes and Functions to Serve as the Basis for Other 'Gx' Packages