Bioconductor Packages

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

Annotations for City of Hope CpG Island Analysis Pipeline

Data normalization by matrix raking

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

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

Datasets and workflows for the Cardinal MSI

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

Pre-processed data for use with the CellMapper package

Evaluate Cellspecific Mixing

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

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

Quantitative comparison of multiple ChIP-seq datasets

ChIP-seq Target Databases for TFEA.ChIP

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

R interface to a subset of OpenBabel functionalities

Cheminformatics Toolkit for R

Chimp and human brain data package

Heat map plotting by genome coordinate

Analysis of single-cell epigenomics datasets with a Shiny App

End-to-End Analysis of Small RNA-Seq Data from Viroids

Detect and Correct Genomic DNA Contamination in RNA-seq Data

Infers clonal composition of a tumor

Simulation of Tumor Clonal Evolution with Realistic Sequencing Noise

Clustering of MS2 Spectra for Metabolite Identification

Data for the CluMSID package

Judging Quality of Clustering Methods using Mutual Information

Coordinated Gene Activity in Pattern Sets

An Investigation Across Different Species and Tissues

VST normalized RNA-Sequencing data with annotations for multiple species samples from Bgee

Complexome Profiling Analysis package

Automated detection tool for spillover errors

Make Complex Heatmaps

Creating and Using (Chemical) Compound Annotation Databases

Functional connections between drugs, genes and diseases as revealed by common gene-expression changes

Create Copy-Number Plots using karyoploteR functionality

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