Biocview "Coverage"

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 graphical interface for the metagene package
A graphical interface for the metagene package
A graphical interface for the metagene package
alpine
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 alternative splicing using RNA-Seq
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
An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
A normalization method for Copy Number Aberration in cancer samples
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 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
An R package for the creation of complex genomic profile plots
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
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
ATAC sequencing Quality Control
BadRegionFinder: an R/Bioconductor package for identifying regions with bad coverage
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
Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Basic peak calling on STARR-seq data
Basic peak calling on STARR-seq data
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)
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
BBCAnalyzer: an R/Bioconductor package for visualizing base counts
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
BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality in somatic mosaicism using next generation sequencing data
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIP-Seq Analysis with Windows
ChIP-Seq Analysis with Windows
ChIP-Seq Analysis with Windows
chipseq: A package for analyzing chipseq data
chipseq: A package for analyzing chipseq data
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
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.
CNVrd2: a read depth-based method to detect and genotype complex common copy number variants from next generation sequencing data.
Computational pipeline for computing probability of modification from structure probing experiment data
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
Copy number calling and SNV classification using targeted short read sequencing
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 targeted sequencing using off-target reads
Copy number information from targeted sequencing using off-target reads
Copy number information from targeted sequencing using off-target reads
Copy number information from targeted sequencing using off-target reads
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 consensus regions inside a group of experiences using genomic positions and genomic ranges
(development for M3D) Identifies differentially methylated regions across testing groups
Differential Analyis of Hi-C Data
Differential Analyis of Hi-C Data
Differential Analyis of Hi-C Data
Differentially Methylated CpG using Hidden Markov Model
Differentially Methylated CpG using Hidden Markov Model
Differentially Methylated Regions caller
Differentially Methylated Regions caller
Distributed computing by file or by range
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
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
Explore and download data from the recount 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
Extract read count signals from bam files
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms
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 SNV/Indel differences between two bam files with near relationship
Find SNV/Indel differences between two bam files with near relationship
functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets
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
Generate HTML or PDF reports for a set of genomic regions or DESeq2/edgeR results
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
Guitar
Guitar
GWAS trait-associated SNP enrichment analyses in genomic intervals
GWAS trait-associated SNP enrichment analyses in genomic intervals
HDF5 back end for DelayedArray objects
HDF5 back end for DelayedArray objects
High Throughput Sequencing Cell Authentication Toolkit
High Throughput Sequencing Cell Authentication Toolkit
Identification of Novel alternative PolyAdenylation Sites (PAS)
Identification of Novel alternative PolyAdenylation Sites (PAS)
Identification of Novel alternative PolyAdenylation Sites (PAS)
Identifies differentially methylated regions across testing groups
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
Infrastructure to work with genomewide position-specific scores
Integrative Analysis and Visualization of Epigenomic Sequencing Data
Integrative Analysis and Visualization of Epigenomic Sequencing Data
Introduce *Ranges to bedtools users
Introduce *Ranges to bedtools users
Introduce *Ranges to bedtools users
Intron-Exon Retention Estimator
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
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 2D Hilbert Curve
Making Enriched Heatmaps
Making Enriched Heatmaps
Making Enriched Heatmaps
Making Enriched Heatmaps
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
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
Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data
Multiple Beta t-Tests
Multiple Beta t-Tests
Optimized Functional Annotation Of ChIP-seq Data
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
Plot customizable linear genomes displaying arbitrary data
Prediction of chromatin looping interactions from ChIP-seq and sequence motifs
Quantify and Annotate Short Reads in R
Quantify and Annotate Short Reads in R
Quantifying Differential Features
Quantitative comparison of multiple ChIP-seq datasets
Quantitative comparison of multiple ChIP-seq datasets
Reliable CNV detection in targeted sequencing applications
Reliable CNV detection in targeted sequencing applications
Reliable CNV detection in targeted sequencing applications
Representation and manipulation of genomic intervals and variables defined along a genome
Representation and manipulation of genomic intervals and variables defined along a genome
Representation and manipulation of genomic intervals and variables defined along a genome
Representation and manipulation of genomic intervals and variables defined along a genome
Representation and manipulation of short genomic alignments
Representation and manipulation of short genomic alignments
Representation and manipulation of short genomic alignments
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
Ribosome Profiling Data Analysis: from BAM to Data Representation and Interpretation
RNA Centric Annotation System
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
Scale4C: an R/Bioconductor package for scale-space transformation of 4C-seq data
Segvis: A package for visualization of high throughout sequencing data along genomic segments
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 Overview of Normalized Expression data
SummarizedExperiment container
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
Tool for converting GFF3 file format data to a GRanges Object
Tools for computational epigenomics
Tools for computational epigenomics
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
TVTB: The VCF Tool Box
TVTB: The VCF Tool Box
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