Biocview "ChIPSeq"

Affinity test for identifying regulatory SNPs
Affinity test for identifying regulatory SNPs
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
Analysis Of Differential Abundance Taking Sample Variation Into Account
Analysis Of Differential Abundance Taking Sample Variation Into Account
AnaLysis routines for ePigenomicS data
AnaLysis routines for ePigenomicS data
Analyze Transcription Factor Enrichment
Analyze Transcription Factor Enrichment
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
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms
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 to produce metagene plots
A package to produce metagene plots
A package to produce metagene plots
Application of t-sne to NGS Genomic Signal Profiles
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 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
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPanalyser: Predicting Transcription Factor Binding Sites
ChIPanalyser: Predicting Transcription Factor Binding Sites
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
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
Chip-seq Signal Quantifier Pipeline
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
chroGPS2: Generation, visualization and differential analysis of epigenome maps
Clustering and Alignment of ChIP-Seq peaks based on their shapes
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
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.
Companion package to chipenrich
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
ComSeq: An ensemble method for RNA-Seq differential analysis
ComSeq: An ensemble method for RNA-Seq differential analysis
Coordinate Covariation Analysis
Coordinate Covariation Analysis
Coordinate Covariation Analysis
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
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
dgeAnalysis
Differential Binding Analysis of ChIP-Seq Peak Data
Differential Binding Estimation for Protein Complexes
Differential Binding of Transcription Factor with ChIP-seq
Differential Epigenetic Coregulation Test
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
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
dPeak (Deconvolution of Peaks in ChIP-seq Analysis)
dPeak (Deconvolution of Peaks in ChIP-seq Analysis)
DynaMO predicts spatiotemporal binding of transcription factors
Empirical Analysis of Digital Gene Expression Data in R
Epigenetic and gene transcription data normalization and integration with mixture models
Epigenomic R-based analysis with hidden Markov models
Epigenomic R-based analysis with hidden Markov models
epigenomic road map adventures
Experimental Design in Differential Abundance analysis
Finding Co-occuring motifs of transcription factor binding sites
Functionality Visualization for Motifs
GC Aware Peak Caller
GC Aware Peak Caller
Gene Set Enrichment For ChIP-seq Peak Data
GeneSet objects from ChIP-Seq experiments
Grey Lists -- Mask Artefact Regions Based on ChIP Inputs
Hi-C Annotation and Graphics Ensemble
iASeq: integrating multiple sequencing datasets for detecting allele-specific events
Identifying Protein Binding Sites in High-Throughput Sequencing Data
Infrastructure for microfluidic oscillatory washing-based ChIP
Interactive Differential Expresion Analysis Browser
Interactive Differential Expresion Analysis Browser
Interactive Differential Expresion Analysis Browser
IP-seq data analysis and vizualization
IP-seq data analysis and vizualization
Learning from DNA to Predict Enhancers
Linear model and normality based normalization and transformation method (Linnorm)
Locus 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
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
Motif Identification and Validation
Motif Identification and Validation
Motifs in Tandem with One Another
Multiple Sample Peak Calling: Using combined evidence from replicates to evaluate ChIP-seq peaks
Normalisation Tools for Inter-Condition Variability of ChIP-Seq Data
Normalisation Tools for Inter-Condition Variability of 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
Nucleosome positioning package for R
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Optimized Functional Annotation Of ChIP-seq Data
Peak Refinement Metric Gathering and Evalutation by Motif Enrichment
pinnacle: Gene set enrichment analysis based on genomic intervals
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
Power Estimation Tool for RNA-Seq and proteomics data
Power Estimation Tool for RNA-Seq and proteomics data
Quality Control Pipeline for ChIP-Seq Data
Quality Control Pipeline for ChIP-Seq Data
Quality Control Pipeline for ChIP-Seq Data
Quality metrics for ChIPseq data
Quality metrics for ChIPseq data
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-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
Recipes using seqsetvis
Replicate oriented Visualization of a genomic region
Replicate oriented Visualization of a genomic region
Replicate oriented Visualization of a genomic region
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
Search for correlation between epigenetic signals and gene expression in TADs
Search for correlation between epigenetic signals and gene expression in TADs
Segvis: A package for visualization of high throughput sequencing data along genomic segments
Set Based Visualizations for Next-Gen Sequencing Data
Set Based Visualizations for Next-Gen Sequencing Data
Shape-based Analysis of Variation in ChIP-seq using Functional PCA
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 tools for the analysis of ChIP-seq data
Subread Sequence Alignment and Counting for R
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
TFregulomeR reveals transcription factors’ context-specific features and functions
TFregulomeR reveals transcription factors’ context-specific features and functions
TFregulomeR reveals transcription factors’ context-specific features and functions
The Genomic STate ANnotation Package
Time course sequencing data analysis
Time course sequencing data analysis
Tools for the Efficient Analysis of High-Resolution Genomics Data
Tools for the Efficient Analysis of High-Resolution Genomics Data
Transcription Factor High Accumulation Zones
Transcription Factor High Accumulation Zones
Triform finds enriched regions (peaks) in transcription factor ChIP-sequencing data
VirtUaL ChIP-Seq data Analysis using Networks
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
Visualization and annotation of read signal over genomic ranges with profileplyr
Visualization and annotation of read signal over genomic ranges with profileplyr