Bioconductor Packages

Clustering Deviation Index (CDI)

Co-expression Modules identification Tool

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.

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

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

A normalization method for Copy Number Aberration in cancer samples

CNE Detection and Visualization

Integration of CellNOptR to add missing links

Addon to CellNOptR: Fuzzy Logic

Copy Number Variant Metrics

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

Data normalization by matrix raking

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

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

Chip-seq Signal Quantifier Pipeline

Genomic coordinates of CTCF binding sites, with orientation

Package for CTDbase data query, visualization and downstream analysis

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

Category Analysis

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

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

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Quantitative comparison of multiple ChIP-seq datasets

Quality metrics for ChIPseq data

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPexoQual

Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data

ChIPseeker for ChIP peak Annotation, Comparison, and Visualization