Version Compatibility

Reference examples tested with: Cell Ranger ATAC 2.1+, Signac 1.13+, Seurat 5.0+, ArchR 1.0.2+, SnapATAC2 2.8+, AMULET 1.1+, scDblFinder 1.16+, scater 1.30+, scvi-tools 1.1+, GenomicRanges 1.54+, JASPAR2024 0.99+, BSgenome.Hsapiens.UCSC.hg38 1.4+, EnsDb.Hsapiens.v86 2.99+, MACS3 3.0+. SnapATAC2 2.8+ uses pp.import_fragments; older 2.5-2.7 used pp.import_data (renamed/removed in 2.9).

Verify before use:

• Python: pip show <package> then help(module.function) to check signatures
• R: packageVersion('<pkg>') then ?function_name to verify parameters
• CLI: <tool> --version then <tool> --help to confirm flags

If code throws unexpected errors, introspect the installed package and adapt rather than retrying.

Single-Cell ATAC-seq

"Process my 10X scATAC data from cellranger output" -> Build a per-cell fragment matrix, compute per-cell QC, dimensionality reduction (TF-IDF + LSI / spectral / autoencoder), cluster, call cluster-level pseudobulk peaks, annotate cell types via gene-activity scores, and integrate with paired scRNA-seq if Multiome.

• R: Signac::CreateChromatinAssay() -> Seurat workflow (TF-IDF + SVD + UMAP + Leiden)
• R: ArchR::createArrowFiles() -> ArchR project (TileMatrix + LSI + UMAP)
• Python: snapatac2.pp.import_fragments() -> SnapATAC2 (spectral / diffusion-map clustering)
• CLI (preprocessing): cellranger-atac count (10X) or chromap (alignment-only fragment files)