Biocview "ChIPSeq"

A GAM based framework for analysis of ChIP-Seq data
A GAM based framework for analysis of ChIP-Seq data
A GAM based framework for analysis of ChIP-Seq data
A graphical interface for the metagene package
A graphical interface for the metagene package
A graphical interface for the metagene package
Analysis Of Differential Abundance Taking Sample Variation Into Account
Analysis Of Differential Abundance Taking Sample Variation Into Account
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps
An interactive tool for visualizing NGS signals and sequence motif densities along genomic features using average plots and heatmaps.
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
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach
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 For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites
A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites
A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites
A package to produce metagene plots
A package to produce metagene plots
A package to produce metagene plots
Association analysis of genomic regions based on permutation tests
Association analysis of genomic regions based on permutation tests
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments or any experiments resulted in large number of chromosome ranges
Bayesian Analysis of ChIP-seq Data
Bayesian Analysis of ChIP-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)
Bayesian hierarchical model for genome-wide profiling of nucleosome positions based on high-throughput short-read data (MNase-Seq data)
Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models
Bayesian Hierarchical Modeling of ChIP-seq Data Through Hidden Ising Models
ChIPexoQual
ChIPexoQual
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
ChIPseeker for ChIP peak Annotation, Comparison, and Visualization
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
ChIP-Seq Statistical Power
ChIP-Seq Statistical Power
ChIP-Seq Statistical Power
ChIPUtils - A package to perform exploratory analysis of ChIP data and most commonly used QC measures
ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
ChIPXpress: enhanced transcription factor target gene identification from ChIP-seq and ChIP-chip data using publicly available gene expression profiles
Clustering and Alignment of ChIP-Seq peaks based on their shapes
Clustering and Alignment of ChIP-Seq peaks based on their shapes
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
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
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.
ComSeq: An ensemble method for RNA-Seq differential analysis
Coverage visualization package for R
Coverage visualization package for R
DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
DChIPRep - Analysis of chromatin modification ChIP-Seq data with replication
debrowser: Interactive Differential Expresion Analysis Browser
debrowser: Interactive Differential Expresion Analysis Browser
debrowser: Interactive Differential Expresion Analysis Browser
de novo motif discovery
de novo motif discovery
de novo motif discovery
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
Differential Binding Analysis of ChIP-Seq Peak Data
Differential Binding Analysis of ChIP-Seq Peak Data
Differential Binding Estimation for Protein Complexes
Differential Binding of Transcription Factor with ChIP-seq
Differential Binding of Transcription Factor with ChIP-seq
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Differential gene expression analysis based on the negative binomial distribution
Dispersion shrinakge for sequencing data.
Dispersion shrinakge for sequencing data.
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DNA IP-seq data analysis
DynaMO predicts spatiotemporal binding of transcription factors
Empirical Analysis of Digital Gene Expression Data in R
Empirical Analysis of Digital Gene Expression Data in R
Epigenetic and gene transcription data normalization and integration with mixture models
Epigenetic and gene transcription data normalization and integration with mixture models
Experimental Design in Differential Abundance analysis
Experimental Design in Differential Abundance analysis
Finding Co-occuring motifs of transcription factor binding sites
Finding Co-occuring motifs of transcription factor binding sites
GC Aware Peak Caller
GC Aware Peak Caller
GC Aware Peak Caller
Gene Set Enrichment For ChIP-seq Peak Data
Gene Set Enrichment For ChIP-seq Peak Data
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
iASeq: integrating multiple sequencing datasets for detecting allele-specific events
iASeq: integrating multiple sequencing datasets for detecting allele-specific events
Identifying Protein Binding Sites in High-Throughput Sequencing Data
Identifying Protein Binding Sites in High-Throughput Sequencing Data
IP-seq data analysis and vizualization
IP-seq data analysis and vizualization
Joint analysis of multiple ChIP-Seq data sets
Learning from DNA to Predict Enhancers
Learning from DNA to Predict Enhancers
Linear model and normality based transformation method (Linnorm)
Linear model and normality based transformation method (Linnorm)
Location overlap analysis for enrichment of genomic ranges
Location overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Locus overlap analysis for enrichment of genomic ranges
Make read coverage plots from BigWig files
Make read coverage plots from BigWig files
Methylation-Based Inference of Regulatory Activity
Metrics to estimate a level of similarity between two ChIP-Seq profiles
Metrics to estimate a level of similarity between two ChIP-Seq profiles
Metrics to estimate a level of similarity between two ChIP-Seq profiles
Motif Identification and Validation
Motif Identification and Validation
Motif Identification and Validation
Multiple Sample Peak Calling: Using combined evidence from replicates to evaluate ChIP-seq peaks
Normalization and difference calling in ChIP-seq data
Normalization and difference calling in ChIP-seq data
Normalization and difference calling in ChIP-seq data
Nucleosome positioning package for R
Nucleosome positioning package for R
Nucleosome positioning package for R
Optimal Gene Extensions From Histone Modification ChIP-seq Data
Optimal Gene Extensions From Histone Modification ChIP-seq Data
Optimal Gene Extensions From Histone Modification ChIP-seq Data
Plot customizable linear genomes displaying arbitrary data
Plot customizable linear genomes displaying arbitrary data
Plot customizable linear genomes displaying arbitrary data
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
Probabilistic inference of ChIP-seq
Probabilistic inference of ChIP-seq
Quality metrics for ChIPseq data
Quality metrics for ChIPseq data
Quantify and Annotate Short Reads in R
Quantify and Annotate Short Reads in R
Quantitative comparison of multiple ChIP-seq datasets
Quantitative comparison of multiple ChIP-seq datasets
R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data
R-based analysis of ChIP-seq And Differential Expression - a tool for integrating a count-based ChIP-seq analysis with differential expression summary data
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
samExploreR package: high-performance read summarisation to count vectors with avaliability of sequencing depth reduction simulation
Segvis: A package for visualization of high throughout sequencing data along genomic segments
Shape-based Analysis of Variation in ChIP-seq using Functional PCA
Shape-based Analysis of Variation in ChIP-seq using Functional PCA
Simulation of ChIP-seq experiments
Simulation of ChIP-seq experiments
StatePaintR: a tool for creating and documenting reproducible chromatin state annotations from StateHub
StatePaintR: a tool for creating and documenting reproducible chromatin state annotations from StateHub
Statistical Testing for ChIP-Seq data sets
Statistical Testing for ChIP-Seq data sets
Statistical Testing for ChIP-Seq data sets
Statistical tools for the analysis of ChIP-seq data
Statistical tools for the analysis of ChIP-seq data
Subread sequence alignment for R
Subread sequence alignment for R
SVM2CRM: support vector machine for cis-regulatory elements detections
SVM2CRM: support vector machine for cis-regulatory elements detections
systemPipeRdata: NGS workflow templates and sample data
systemPipeR: NGS workflow and report generation environment
systemPipeR: NGS workflow and report generation environment
The genomic STate ANnotation package
The genomic STate ANnotation package
Time course sequencing data analysis
Time course sequencing data analysis
Time course sequencing data analysis
Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data
Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data
VirtUaL ChIP-Seq data Analysis using Networks
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