Biocview "Coverage"

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing

Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface

A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)

A container (S4 class) for matrix-like assays

Additional functions for working with ChIP-Seq data

A fluent interface for manipulating GenomicRanges

A graphical interface for the metagene package

alpine

Analysis of alternative splicing using RNA-Seq

Analysis of Alternative Splicing Using RNA-Seq

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

Analysis of Transposable Elements

Analysis tools for Single Molecule Footprinting (SMF) data

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

An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

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

A normalization method for Copy Number Aberration in cancer samples

An R package facilitating analysis of RNA modifications, structures, and interactions

An R package for analysis of massive parallel sequencing based RNA structure probing data

An R package for the creation of complex genomic profile plots

An R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates

A package to produce metagene plots

ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events

Assess epigenetic heterogeneity with proportion of intermediate methylation

ATAC-seq Quality Control

A Tool for Customizable and Reproducible Plotting of Sequencing Coverage Data

BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage

Base resolution DNA methylation data analysis

Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

Basic4CSim: Simulation of 4C-seq data

Basic peak calling on STARR-seq data

Bayesian clustering and imputationa of single cell methylomes

Bayesian Enrichment Estimation in R

Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)

Bayesian modelling of cell-to-cell DNA methylation heterogeneity

BBCAnalyzer: an R/Bioconductor package for visualizing base counts

Bias Awared Peak Calling and Quantification for MeRIP-Seq

Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import

Binding site defintion based on iCLIP data

Bisulfite-seq OutlieR mEthylation At singLe-sIte reSolution

BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data

Calculate JCC Scores

Calculate strandness information of a bam file

CellRanger Input/Output

Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPexoQual

ChIP-Seq Analysis with Windows

chipseq: A package for analyzing chipseq data

ChIP-Seq data scaling according to spike-in control

ChIPUtils - A package to perform exploratory analysis of ChIP data and most commonly used QC measures

Client for GREAT Analysis

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

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs

Computational pipeline for computing probability of modification from structure probing experiment data

Compute coverage matrices from recount quickly using bwtool

Container for PhIP-Seq Experiments

Context-Aware Transcript Quantification from Long Read RNA-Seq data

Conveniently access PyRanges functionalities from Bioconductor

Copy number calling and SNV classification using targeted short read sequencing

Copy number information from ChIP_seq using off-target reads off-target reads

Copy number information from targeted sequencing using off-target reads

Core Engine for NxtIRF: a User-Friendly Intron Retention and Alternative Splicing Analysis using the IRFinder Engine

Create Copy-Number Plots using karyoploteR functionality

DegNorm: degradation normalization for RNA-seq data

Delineate outstanding genomic zones of differential gene activity

Design Degenerate Oligos from a Multiple DNA Sequence Alignment

Detecting abberant splicing events from RNA-sequencing data

Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges

Detection of de novo deletion in targeted sequencing trios

(development for M3D) Identifies differentially methylated regions across testing groups

Differential Analyis of Hi-C Data

Differential Co-expression Analysis

Differential Enrichment Scan 2

Differentially Methylated CpG using Hidden Markov Model

Differentially Methylated Cytosines via a Bayesian Functional Approach

Differentially Methylated Regions caller

Differential pattern analysis for Ribo-seq data

Discriminant Analysis for Evolutionary Inference

Distributed computing by file or by range

DNA IP-seq data analysis

Empirical Analysis of Digital Gene Expression Data in R

Environment for Gene Expression Searching Combined with Functional Enrichment Analysis

Estimates Isoform Specific RPF Footprint Densities

Explore and download data from the recount3 project

Explore and download data from the recount project

Extract read count signals from bam files

Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

Fast and efficient summarization of single cell whole genome bisulfate data

Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files

Find breakpoints in Strand-seq data

Finding differentially expressed unannotated genomic regions from RNA-seq data

Find RAre Splicing Events in RNA-Seq Data

Finds DAMEs - Differential Allelicly MEthylated regions

Find SNV/Indel differences between two bam files with near relationship

functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets

Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results

Generate Quality Surrogate Variable Analysis for Degradation Correction

GenomicDistributions: fast analysis of genomic intervals with Bioconductor

GenomicOperations

Graphical User Interface for High Performance BAM-based binary alternative splicing event quantitation, differential analysis, and visualisation

GREAT Analysis - Functional Enrichment on Genomic Regions

Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

GWAS trait-associated SNP enrichment analyses in genomic intervals

HDF5 backend for DelayedArray objects

HDF5 datasets as array-like objects in R

Heatmaps of Stack Profiles from Epigenetic Signals

High Throughput Sequencing Cell Authentication Toolkit

HMMRATAC - a semi-supervised machine learning approach for identifying open chromatin regions from ATAC-Seq data using Hidden Markov Models

Identifies differentially methylated regions across testing groups

igvShiny: a wrapper of Integrative Genomics Viewer (IGV - an interactive tool for visualization and exploration integrated genomic data)

Imputation-guided re-construction of complete methylomes from WGBS data

Infrastructure to work with genomewide position-specific scores

InPAS: a bioconductor package for the identification of novel alternative PolyAdenylation Sites (PAS) using RNA-seq data

Integrative Analysis and Visualization of Epigenomic Sequencing Data

interactive analysis and visualization of alternative splicing in R

Interactive graphical application for clinical assessment of sequence coverage at the base-pair level

Interactive microbiome analysis toolkit

interactive visualization of genomics data

Introduce *Ranges to bedtools users

Intron-Exon Retention Estimator

Investigation of Fragmentation Conditions in Top-Down Proteomics

Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs

m6Aexpress-BHM: Predicting m6A regulation of gene expression in multiple-groups context by a Bayesian Hierarchical Mixture model

Make read coverage plots from BigWig files

Making 2D Hilbert Curve

Making Enriched Heatmaps

megadepth: BigWig and BAM related utilities

Methylation array and sequencing spatial analysis methods

Methylation-Based Inference of Regulatory Activity

Microbiome Data Simulation

Model higher-order methylation profiles

Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

Multimodal Mediation Analysis

Multiple Beta t-Tests

Multiplex PCR Primer Design and Analysis

Negative Binomial Additive Model for RNA-Seq Data

Negative Binomial Beta t-Test

Negative binomial model for scRNA-seq

Nucleosome positioning package for R

Open Reading Frames in Genomics

Optimized Functional Annotation Of ChIP-seq Data

Peak Calling and differential analysis for MeRIP-Seq

Plot customizable linear genomes displaying arbitrary data

Plots and annotation for choosing BrainFlow target probe sequence

Power Estimation Tool for RNA-Seq and proteomics data

Predicting context-specific m6A regulation of gene expression

Predicting context-specific m6A regulation of gene expression combinding m6A reader binding information

Prioritization of potentially bioactive metabolic features from epidemiological and environmental metabolomics datasets

Quantify and Annotate Short Reads in R

Quantifying Differential Features

Quantitative comparison of multiple ChIP-seq datasets

R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts

Reference-guided isoform reconstruction and quantification for long read RNA-Seq data

Reliable CNV detection in targeted sequencing applications

Replicate oriented Visualization of a genomic region

Representation and manipulation of genomic intervals

Representation and manipulation of genomic intervals; demo with github actions binary generation

Representation and manipulation of short genomic alignments

Retrotransposed transcript detection from structural variants

RiboseQC, a Comprehensive Ribo-Seq Analysis Tool

Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation

Ribosome Profiling Quality Control

RLSeq: An analysis package for R-loop mapping data

RNA Centric Annotation System

runibic: row-based biclustering algorithm for analysis of gene expression data in R

Run `magic-impute` on scRNA Seq dataset in R

Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data

Seamless visualization of complex genomic variations in GMOs and edited cell lines

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

Set of tools to identify periodic occurrences of k-mers in DNA sequences

Set of tools to make V-plots and compute footprint profiles

Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)

Significance-based Modules Integrating the Transcriptome and Epigenome

Single-Cell Analysis Toolkit for Gene Expression Data in R

Single Cell Overview of Normalized Expression data

Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

Spatial Transcriptomics Analysis

Statistical Utility for RBP (RNA binding protein) Functions

Subtype Identification with Survival Data

SummarizedExperiment container

systemPipeRdata: Workflow templates and sample data

systemPipeR: NGS workflow and report generation environment

systemPipeR: Workflow Environment for Data Analysis and Report Generation

TARgeted SEQuencing Experiment Quality Control

Tidy Meta Profiles using Bioconductor and the Tidyverse

Toolkit for Single-Cell Velocity

Tools for computational epigenomics

Tools for Managing Seurat Objects

Tools for the Efficient Analysis of High-Resolution Genomics Data

Tornado Plot

Transcript abundance linear modeling from compressed coverage information

Transcript Annotation Tool (TransAT): an R package for retrieving annotations for transcript specific genetic variants

Transcription Factor High Accumulation Zones

Transcriptome-guided quality assessment of m6A-seq data

TSS sequencing data analysis

TVTB: The VCF Tool Box

UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

uORF prediction in R

Utilities for Handling Single-Cell Droplet Data

Utilities to create and use an Ensembl based annotation database

Utilities to create and use Ensembl-based annotation databases

Visualise ChIP-seq, MNase-seq and motif occurrence as aggregate plots Summarised Over Grouped Genomic Intervals

Visualization and annotation of read signal over genomic ranges with profileplyr

What the Package Does (One Line, Title Case)

XCI-inference

Biocview "Coverage"

R Package Documentation

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