Bioconductor Packages

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

ATAC-seq Quality Control

Transcription Factor Enrichment Analysis for ATAC-seq

A normalization method for Copy Number Aberration in cancer samples

Identifies false positives of CNV calling tools by using SNV calls

Copy Number Visualization

Infers clonal composition of a tumor

Create Copy-Number Plots using karyoploteR functionality

Genomic Visualizations in R

Gene Break Detection

A fast hierarchical graph-based clustering method

Call wide peaks for sequencing data

Quantitative DNA Sequencing for Chromosomal Aberrations

Quasispecies Diversity

Bioinformatics pipelines based on Rcwl

A normalization and copy number estimation method for single-cell DNA sequencing

Semi-parametric simulation tool for bulk and single-cell RNA sequencing data

Mutational Signature Estimation for Single Samples

TVTB: The VCF Tool Box

Yet Another Package for Signature Analysis

Find breakpoints in Strand-seq data

compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots

Differential Expression Analysis for RNA-seq data through a robust variance component test

Decomposition of individual tumors into mutational signatures by signature refitting

An Easy-to-use Systematic pipeline for ATACseq data analysis

Extract Fragmentomics Features and Mutational Status

A High-Throughput and Extensible Toolkit for Processing FASTQ Data

Plot customizable linear genomes displaying arbitrary data

Summarize, Analyze and Visualize MAF Files

Microbiome Data Simulation

Mixture Nested Effects Models

Inferring unobserved perturbations from gene expression data

Visual Exploration of Omic Datasets Using a Shiny App

Association analysis of genomic regions based on permutation tests

RegioneReloaded: Multiple Association for Genomic Region Sets

Semi-Supervised Mixture Model

Targeted sequencing panel design based on mutation hotspots

spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

RNA-seq data analysis using the Poisson-Tweedie family of distributions

uSORT: A self-refining ordering pipeline for gene selection