Bioconductor Packages

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

Cytometry dATa anALYSis Tools

plot bayesian network inferred from gene expression data based on enrichment analysis results

Case Control Allele Frequency Estimation

Co-expression Modules identification Tool

CGHbase: Base functions and classes for arrayCGH data analysis.

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

A Package for CLL Gene Expression Data

Methylation data of primary CLL samples in PACE project

A normalization method for Copy Number Aberration in cancer samples

CNE Detection and Visualization

Integration of CellNOptR to add missing links

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

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

Coordinate Covariation Analysis

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

COexpression Tables ANalysis

CRC cell line dataset

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

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

A mass spectrometry imaging toolbox for statistical analysis

Read and write mass spectrometry imaging files

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

Construct Benchmarks for Single Cell Analysis Methods

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

Quantitative comparison of multiple ChIP-seq datasets

ChIP-seq Target Databases for TFEA.ChIP

ChIPXpress Pre-built Databases

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPexoQual

Identifying Protein Binding Sites in High-Throughput Sequencing Data

Simulation of ChIP-seq experiments