Use this skill when the user is analyzing AtlasXomics spatial epigenomics data, including spatial ATAC-seq, gene activity matrices, motif enrichment, fragment files, or data mentioning AtlasXomics, DBiT-seq, or spatial chromatin accessibility. Use it for QC, clustering, differential analysis, and cell type annotation of spatial ATAC data.
Use this skill for AtlasXomics platform detection, workflow order, step execution, and spatial ATAC-seq analysis.
AtlasXomics, DBiT-seq, or spatial ATACgene_activity, motif, or .fragments filescombined_sm_ge.h5ad, combined_sm_motifs.h5ad, or ArchR project directoriesIf the platform is still unclear, ask before executing platform-specific steps.
If the environment supports redeem_package, install the AtlasXomics package before analysis:
package_code: 2428814b149447a4c354b3cb4520095b77955bf99cb3eedfef20b920a2a7d3d7package_version_id: 405If redeem_package is unavailable, continue with the repo-local docs and the current environment.
Read main.md for the step plan, then load each step doc before executing it.
combined_sm_ge.h5ad: Gene activity scores for all spots/cells. Recommended for analyses. .X matrix contains gene activity imputed from chromatin accessibility.combined_sm_motifs.h5ad: Motif enrichment scores (870 motifs). .X matrix contains TF motif enrichment.Internal Workspace (13502):
/chromap_outs/[Run_ID]/chromap_output/fragments.tsv.gz/Images_spatial/[Run_ID]/spatial/snap_outs/[project_name]/Collaborator Workspaces:
.../Raw_Data/[Run_ID]/chromap_output/fragments.tsv.gz.../Raw_Data/[Run_ID]/spatial.../Processed_Data/[project_name]If latch-workflows, latch-plots-ui, or latch-data-access are available, prefer them for:
If those sibling skills are not available, use the local wf/, steps/, and README.md docs directly.