Cell Ranger ATAC
Developed by 10x Genomics, this tool is used for processing single-cell ATAC-seq data. It performs demultiplexing, alignment, and peak calling to generate outputs that help identify accessible chromatin regions at a single-cell level.
ArchR
ArchR is an integrated R-based pipeline for analyzing single-cell ATAC-seq data. It enables users to conduct clustering, trajectory inference, and integrative analyses, such as correlating chromatin accessibility with gene expression from scRNA-seq.
HOMER
HOMER is a suite of tools that can be used to analyze ATAC-seq data for motif discovery and functional annotation. It also provides visualization tools, including tools for exploring chromatin accessibility profiles across multiple samples.
MACS2
A widely used peak-calling tool, MACS2 can analyze bulk ATAC-seq data to identify regions of open chromatin. It models fragment sizes to accurately identify regions of interest, and is effective in comparing conditions.
Juicer
Juicer is an all-in-one pipeline for processing Hi-C data, from raw sequence files to normalized interaction matrices. Developed by the Aiden Lab, Juicer provides high-quality data normalization and visualization options, making it a popular choice for 3D genome studies.
HiC-Pro
HiC-Pro is a flexible pipeline for the processing and analysis of Hi-C sequencing data. It includes modules for quality control, filtering, alignment, and contact matrix generation. It also supports different restriction enzyme-based protocols.
HiGlass
HiGlass is an interactive visualization tool designed for exploring Hi-C datasets, along with other genomic data types. It allows for seamless integration and visualization of large datasets, helping users interpret spatial organization of the genome.
Juicebox
Juicebox is a companion visualization tool for Juicer. It provides an interactive environment to explore Hi-C contact maps and extract insights on 3D genome conformation, such as chromatin loops and topologically associated domains (TADs).
SEACR (Sparse Enrichment Analysis for CUT&RUN)
SEACR is a peak-calling algorithm optimized for CUT&RUN data. It leverages the low background noise characteristic of CUT&RUN to identify enriched regions with high specificity and sensitivity, making it ideal for studying histone modifications and transcription factor binding.
CUT&RUNTools
CUT&RUNTools is an R-based suite that provides an analysis pipeline for pre-processing CUT&RUN data, including alignment, peak calling, and visualization. It can integrate with publicly available datasets to contextualize findings.
LanceOtron
LanceOtron is a web-based tool designed to work with CUT&RUN, CUT&Tag, and ChIP-seq data for peak calling. It uses machine learning to classify potential binding sites and identify enriched regions, giving researchers flexibility in tuning stringency and sensitivity.
Signac
Signac is an R package designed for the analysis of chromatin accessibility data generated using single-cell sequencing technologies. It works alongside Seurat to allow users to integrate scATAC-seq and scRNA-seq data, providing insights into gene regulation and epigenetic landscapes.
Genome Browser (UCSC or IGV)
The UCSC Genome Browser and IGV (Integrative Genomics Viewer) are essential tools for visualizing genomic data. Users can upload ATAC-seq, Hi-C, CUT&RUN, or other data types to interpret chromatin features, enhancer activity, or transcription factor binding across different regions of the genome.
ArchR
As mentioned above, ArchR is versatile and can be used to integrate multiomic datasets, such as ATAC-seq and RNA-seq. It has modules for motif enrichment analysis, pseudotime trajectory estimation, and the integration of single-cell accessibility data with gene expression.
DeepTools
DeepTools is a versatile toolkit used for visualizing and analyzing data from epigenomic assays such as ATAC-seq, ChIP-seq, and RNA-seq. It allows users to generate plots of read density, profile heatmaps, and compare conditions across multiple datasets.
BEDTools
BEDTools is a powerful software suite that facilitates genomic interval manipulation and analysis. It is widely used to intersect, subtract, and merge genomic features from different epigenomic datasets to understand overlapping or unique features.
Galaxy
Galaxy is an open-source web-based platform that provides access to numerous bioinformatic tools, including those for processing ATAC-seq, Hi-C, and ChIP-seq data. It allows researchers to create, share, and reproduce data analysis workflows without requiring programming skills.