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Documentation
Installation
User Guide
Tutorials
Bulk ATAC-seq Analysis
Visualize the Bulk ATAC-seq
Bulk ATAC-seq footprinting — Bcell vs Tcell with TOBIAS + ArchR
OTX2 case study — visualization tutorial
Differential peak accessibility — ATAC-seq in OTX2 knockdown
Hi-C basics — Drosophila S2 contact matrix with
epione.bulk.hic
/
epione.upstream
Upstream tutorial: bulk ATAC-seq
Upstream tutorial: ChIP-seq
Upstream tutorial: CUT&RUN
Single-cell ATAC-seq Analysis
scATAC-seq preprocessing
Integrate Multi Samples
ArchR-style Iterative LSI
Peak-to-Gene Linkage
Motif and TF activity with chromVAR
CCA-based celltype label transfer (scRNA → scATAC)
TF footprint analysis — ArchR-style on BMMC
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