Biocview "ATACSeq"

A/B compartment inference from ATAC-seq and methylation array data
A/B compartment inference from ATAC-seq and methylation array data
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
Analysis of single-cell epigenomics datasets with a Shiny App
Analysis of single-cell epigenomics datasets with a Shiny App
AnaLysis routines for ePigenomicS data
AnaLysis routines for ePigenomicS data
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 R Package for Integrating and Visualizing Single-Cell and Bulk Data to Resolve Regulatory Elements
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
ATAC-seq Quality Control
ATAC-seq Quality Control
ATACtion is the ACTIONet extension for sc/sn-ATAC-seq data analysis
Bias-free Footprint Enrichment Test
Bias-free Footprint Enrichment Test
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
Comparison, Benchmarking & QC of Epigenetic Datasets
Coordinate Covariation Analysis
Coordinate Covariation Analysis
Coordinate Covariation Analysis
Differential Binding Analysis of ChIP-Seq Peak Data
Differential cell-type-specific allelic imbalance
Differential Epigenetic Coregulation Test
Epigenomic R-based analysis with hidden Markov models
Epigenomic R-based analysis with hidden Markov models
Exploratory Analysis of ATAC-seq data
Fast Sequence Mapping in High-Throughput shRNA and CRISPR Screens
find influential TF and Target based on multi-omics data
Generation of null ranges via bootstrapping or covariate matching
GRaNIE: Reconstruction cell type specific gene regulatory networks including enhancers using chromatin accessibility and RNA-seq data
Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq
Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq
Identifying genetic trait/phenotype relevant cell type/state at single cell resolution
Identifying genetic trait/phenotype relevant cell type/state at single cell resolution
Inferring unobserved perturbations from gene expression data
IReNA
Iterative Differential Clustering for single-cell
MACS: Model-based Analysis for ChIP-Seq
Microbiome Data Simulation
Mixture Nested Effects Models
Mixture Nested Effects Models
PCAtools: Everything Principal Components Analysis
pinnacle: Gene set enrichment analysis based on genomic intervals
Precict cis-co-accessibility from single-cell chromatin accessibility data
Predict cis-co-accessibility from single-cell chromatin accessibility data
Predict cis-co-accessibility from single-cell chromatin accessibility data
Replicate oriented Visualization of a genomic region
Replicate oriented Visualization of a genomic region
Replicate oriented Visualization of a genomic region
scDblFinder
ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion
Set of tools to make V-plots and compute footprint profiles
Set of tools to make V-plots and compute footprint profiles
spatialHeatmap
spatialHeatmap
The slim version of signac
Tools for the Efficient Analysis of High-Resolution Genomics Data
Tools for the Efficient Analysis of High-Resolution Genomics Data
Transcription Factor Enrichment Analysis for ATAC-seq
Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
Utilities for ATACseq QC, differential accessibility, and integration