Biocview "ATACSeq"

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

Analysis of single-cell epigenomics datasets with a Shiny App

AnaLysis routines for ePigenomicS data

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 creation of complex genomic profile plots

ATAC-seq Quality Control

ATACtion is the ACTIONet extension for sc/sn-ATAC-seq data analysis

Bias-free Footprint Enrichment Test

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

Comparison, Benchmarking & QC of Epigenomic Datasets

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

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

functional Canonical Correlation Analysis to evaluate Covariance between nucleic acid sequencing datasets

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

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

PCAtools: Everything Principal Components Analysis

Precict cis-co-accessibility from single-cell chromatin accessibility data

Predict cis-co-accessibility from single-cell chromatin accessibility data

Processing Various Types of Data on GEO and TCGA

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

spatialHeatmap

spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions

The slim version of signac

Tools for Assessing Clustering

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

Utilities for ATACseq QC, differential accessibility, and integration

Biocview "ATACSeq"

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