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

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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