Biocview "Coverage"

Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing
Absolute Copy Number Estimation from Low-coverage Whole Genome Sequencing
Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
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 complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)
A fluent interface for manipulating GenomicRanges
A fluent interface for manipulating GenomicRanges
A graphical interface for the metagene package
A graphical interface for the metagene package
alpine
alpine
Analysis of alternative splicing using RNA-Seq
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 Cap Analysis of Gene Expression (CAGE) data using Bioconductor
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
An Easy-to-use Systematic pipeline for ATACseq data analysis
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
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 and copy number estimation method for single-cell DNA sequencing
A normalization method for Copy Number Aberration in cancer samples
An R package for analysis of massive parallel sequencing based RNA structure probing data
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 for the creation of complex genomic profile plots
A package to produce metagene plots
A package to produce metagene plots
A package to produce metagene plots
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events
Assess epigenetic heterogeneity with proportion of intermediate methylation
Assess epigenetic heterogeneity with proportion of intermediate methylation
ATAC-seq Quality Control
ATAC-seq Quality Control
ATAC-seq Quality Control
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
Base resolution DNA methylation data analysis
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 clustering and imputationa of single cell methylomes
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
Bayesian hierarchical model for genome-wide nucleosome positioning with high-throughput short-read data (MNase-Seq)
BBCAnalyzer: an R/Bioconductor package for visualizing base counts
Bias Awared Peak Calling and Quantification for MeRIP-Seq
Bias Awared Peak Calling and Quantification for MeRIP-Seq
Bias Awared Peak Calling and Quantification for MeRIP-Seq
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
Binary alignment (BAM), FASTA, variant call (BCF), and tabix file import
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
Calculate strandness information of a bam file
Calculate strandness information of a bam file
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms
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
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPexoQual
ChIPexoQual
ChIP-Seq Analysis with Windows
ChIP-Seq Analysis with Windows
chipseq: A package for analyzing chipseq data
chipseq: A package for analyzing chipseq data
ChIP-Seq data scaling according to spike-in control
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
Client for GREAT Analysis
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
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
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 Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
Computational pipeline for computing probability of modification from structure probing experiment data
Computational pipeline for computing probability of modification from structure probing experiment data
Compute coverage matrices from recount quickly using bwtool
Conveniently access PyRanges functionalities from Bioconductor
Copy number calling and SNV classification using targeted short read sequencing
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
Copy number information from targeted sequencing using off-target reads
Create Copy-Number Plots using karyoploteR functionality
Create Copy-Number Plots using karyoploteR functionality
DegNorm: degradation normalization for RNA-seq data
Delineate outstanding genomic zones of differential gene activity
Delineate outstanding genomic zones of differential gene activity
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Detection of consensus regions inside a group of experiences using genomic positions and genomic ranges
Detection of de novo deletion in targeted sequencing trios
Detection of de novo deletion in targeted sequencing trios
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 Analysis of Hi-C Data
Differential Co-expression Analysis
Differential Co-expression Analysis
Differential Enrichment Scan 2
Differential Enrichment Scan 2
Differentially Methylated CpG using Hidden Markov Model
Differentially Methylated CpG using Hidden Markov Model
Differentially Methylated Cytosines via a Bayesian Functional Approach
Differentially Methylated Cytosines via a Bayesian Functional Approach
Differentially Methylated Regions caller
Differentially Methylated Regions caller
Distributed computing by file or by range
Distributed computing by file or by range
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
Empirical Analysis of Digital Gene Expression Data in R
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis
Epigenomic R-based analysis with hidden Markov models
Epigenomic R-based analysis with hidden Markov models
Explore and download data from the recount3 project
Explore and download data from the recount project
Explore and download data from the recount project
Extract read count signals from bam files
Extract read count signals from bam files
Fast and efficient summarization of generic bedGraph files from Bisufite sequencing
Fast and efficient summarization of generic bedGraph files from Bisufite sequencing
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files
Fast Reading and Processing of Common Gene Annotation and Next Generation Sequencing Format Files
Find breakpoints in Strand-seq data
Find breakpoints in Strand-seq data
Find breakpoints in Strand-seq data
Finding differentially expressed unannotated genomic regions from RNA-seq data
Finding differentially expressed unannotated genomic regions from RNA-seq data
Find RAre Splicing Events in RNA-Seq Data
Find RAre Splicing Events in RNA-Seq Data
Find RAre Splicing Events in RNA-Seq Data
Finds DAMEs - Differential Allelicly MEthylated regions
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 HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
GenomicOperations
GenomicOperations
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
GWAS trait-associated SNP enrichment analyses in genomic intervals
HDF5 backend for DelayedArray objects
HDF5 backend for DelayedArray objects
High Throughput Sequencing Cell Authentication Toolkit
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
Imputation-guided re-construction of complete methylomes from WGBS data
Imputation-guided re-construction of complete methylomes from WGBS data
Imputation-guided re-construction of complete methylomes from WGBS data
Infrastructure to work with genomewide position-specific scores
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
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
Integrative Analysis and Visualization of Epigenomic Sequencing Data
Interactive graphical application for clinical assessment of sequence coverage at the base-pair level
Interactive microbiome analysis toolkit
Interactive microbiome analysis toolkit
interactive visualization of genomics data
Introduce *Ranges to bedtools users
Introduce *Ranges to bedtools users
Intron-Exon Retention Estimator
Intron-Exon Retention Estimator
Investigation of Fragmentation Conditions in Top-Down Proteomics
Investigation of Fragmentation Conditions in Top-Down Proteomics
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Loci2path: regulatory annotation of genomic intervals based on tissue-specific expression QTLs
Make read coverage plots from BigWig files
Make read coverage plots from BigWig files
Making 2D Hilbert Curve
Making 2D Hilbert Curve
Making 2D Hilbert Curve
Making Enriched Heatmaps
Making Enriched Heatmaps
Making Enriched Heatmaps
Methylation array and sequencing spatial analysis methods
Methylation array and sequencing spatial analysis methods
Methylation-Based Inference of Regulatory Activity
Methylation-Based Inference of Regulatory Activity
Model higher-order methylation profiles
Model higher-order methylation profiles
Model higher-order methylation profiles
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
Multiple Beta t-Tests
Multiple Beta t-Tests
Multiplex PCR Primer Design and Analysis
Multiplex PCR Primer Design and Analysis
Negative Binomial Additive Model for RNA-Seq Data
Negative Binomial Additive Model for RNA-Seq Data
Nucleosome positioning package for R
Nucleosome positioning package for R
Nucleosome positioning package for R
Nucleosome positioning package for R
Open Reading Frames in Genomics
Open Reading Frames in Genomics
Open Reading Frames in Genomics
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Plot customizable linear genomes displaying arbitrary data
Plot customizable linear genomes displaying arbitrary data
Plots and annotation for choosing BrainFlow target probe sequence
Plots and annotation for choosing BrainFlow target probe sequence
Power Estimation Tool for RNA-Seq and proteomics data
Power Estimation Tool for RNA-Seq and proteomics data
Produces Summaries and Plots of Features Distributed Across Genomes
Quantify and Annotate Short Reads in R
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
R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
R/Bioconductor Package for interfacing with Snaptron for rapid querying of expression counts
Reliable CNV detection in targeted sequencing applications
Reliable CNV detection in targeted sequencing applications
Reliable CNV detection in targeted sequencing applications
Replicate oriented Visualization of a genomic region
Replicate oriented Visualization of a genomic region
Replicate oriented Visualization of a genomic region
Representation and manipulation of genomic intervals
Representation and manipulation of genomic intervals
Representation and manipulation of short genomic alignments
Representation and manipulation of short genomic alignments
RiboseQC, a Comprehensive Ribo-Seq Analysis Tool
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
Ribosome Profiling Quality Control
Ribosome Profiling Quality Control
RNA Centric Annotation System
RNA Centric Annotation System
runibic: row-based biclustering algorithm for analysis of gene expression data in R
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
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 analyze ATAC-seq data
Set of tools to identify periodic occurrences of k-mers in DNA sequences
Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
Shiny app for canonical and back splicing analysis (i.e. circular and mRNA analysis)
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Significance-based Modules Integrating the Transcriptome and Epigenome
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single Cell Overview of Normalized Expression data
Single Cell Overview of Normalized Expression data
Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data
Spatial Transcriptomics Analysis
Spatial Transcriptomics Analysis
Subtype Identification with Survival Data
SummarizedExperiment container
SummarizedExperiment container
SummarizedExperiment container
systemPipeRdata: NGS workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: NGS workflow and report generation environment
TARgeted SEQuencing Experiment Quality Control
TARgeted SEQuencing Experiment Quality Control
Tidy Meta Profiles using Bioconductor and the Tidyverse
Tools for computational epigenomics
Tools for computational epigenomics
Tools for the Efficient Analysis of High-Resolution Genomics Data
Tools for the Efficient Analysis of High-Resolution Genomics Data
Transcript abundance linear modeling from compressed coverage information
Transcription Factor High Accumulation Zones
Transcription Factor High Accumulation Zones
Transcriptome-guided quality assessment of m6A-seq data
TVTB: The VCF Tool Box
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 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
Utilities to create and use Ensembl-based annotation databases
Utilities to create and use Ensembl-based annotation databases
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
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
Visualization and annotation of read signal over genomic ranges with profileplyr
What the Package Does (One Line, Title Case)
What the Package Does (One Line, Title Case)
XCI-inference
XCI-inference