Biocview "DNASeq"

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

A fast hierarchical graph-based clustering method

Analysis Of Differential Abundance Taking Sample and Scale Variation Into Account

Analysis Of Differential Abundance Taking Sample Variation Into Account

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

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

A normalization method for Copy Number Aberration in cancer samples

A Software Suite for Shallow Sequencing Copy Number Analysis

Association analysis of genomic regions based on permutation tests

ATAC-seq Quality Control

A tool for differential expression analysis and DEGs based investigation to complex diseases by bi-clustering analysis

Bioinformatics pipelines based on Rcwl

Call wide peaks for sequencing data

Clonal ordering and visualization

coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns

coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns.

CopyKit

Copy Number Visualization

Create Copy-Number Plots using karyoploteR functionality

Cut rDNA Sequences Into Domains Using Covariance Models

Decomposition of individual tumors into mutational signatures by signature refitting

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

Dual redundant reference sequencing

Find breakpoints in Strand-seq data

Gene Break Detection

Genomic Visualizations in R

Identifies false positives of CNV calling tools by using SNV calls

Identify Different Architectures of Sequence Elements

Inferring unobserved perturbations from gene expression data

Infers clonal composition of a tumor

Interface to Call Programs from Infernal RNA Covariance Model Package

Mean Alterations Using Discrete Expression

Microbiome Data Simulation

Mixture Nested Effects Models

Mutation Mapping Analysis Pipeline for Pooled RNA-Seq

NGScopy: Detection of Copy Number Variations in Next Generation Sequencing sequencing

Plot customizable linear genomes displaying arbitrary data

Quantifying Differential Features

Quantitative DNA Sequencing for Chromosomal Aberrations

Quasispecies Diversity

samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation

Sample Size Calculation for RNA-Seq Experimental Design

Segvis: A package for visualization of high throughput sequencing data along genomic segments

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

Semi-Supervised Mixture Model

spatialHeatmap

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

Statistical Utility for RBP (RNA binding protein) Functions

Subclonal copy number and LOH prediction from whole genome sequencing of tumours

Summarize, Analyze and Visualize MAF Files

"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data"

Transcription Factor Enrichment Analysis for ATAC-seq

TVTB: The VCF Tool Box

Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis

uSORT: A self-refining ordering pipeline for gene selection

Visual comparison of mutational processes in a set of tumors

Visual Exploration of Omic Datasets Using a Shiny App

Yet Another Package for Signature Analysis

Biocview "DNASeq"

R Package Documentation

Browse R Packages

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