├── .gitignore ├── LICENSE ├── README.md ├── clustering ├── 01-BasicFeatureFiltering.ipynb ├── 02-HighlyVariableFeatureSelection.ipynb ├── 03a-GeneratemCHAdata.ipynb ├── 03b-GeneratemCGAdata.ipynb ├── 04a-PreclusteringAndClusterEnrichedFeatures-mCH.ipynb ├── 04b-PreclusteringAndClusterEnrichedFeatures-mCG.ipynb ├── 05a-Decomposition-mCH.ipynb ├── 05b-Decomposition-mCG.ipynb ├── 06-Embedding.ipynb ├── 07-Clustering.ipynb ├── 08-Plot.ipynb └── config │ ├── 01.yaml │ ├── 02.yaml │ ├── 03a.yaml │ ├── 03b.yaml │ ├── 04a.yaml │ ├── 04b.yaml │ ├── 05a.yaml │ ├── 05b.yaml │ ├── 06.yaml │ ├── 07.yaml │ └── 08.yaml ├── dissection_region_ccf ├── CEMBA.itksnap ├── CEMBA_region.nii.gz ├── CEMBA_region.nrrd.gz ├── CEMBA_region_anno_itksnap.txt ├── README.md ├── allen_ccf.tgz └── ply │ ├── 10A.ply │ ├── 10B.ply │ ├── 10C.ply │ ├── 10D.ply │ ├── 10E.ply │ ├── 10F.ply │ ├── 10G.ply │ ├── 10H.ply │ ├── 10J.ply │ ├── 11A.ply │ ├── 11B.ply │ ├── 11C.ply │ ├── 11D.ply │ ├── 11E.ply │ ├── 11F.ply │ ├── 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│ ├── 7F.ply │ ├── 7G.ply │ ├── 7H.ply │ ├── 7J.ply │ ├── 8A.ply │ ├── 8B.ply │ ├── 8C.ply │ ├── 8D.ply │ ├── 8E.ply │ ├── 8F.ply │ ├── 8G.ply │ ├── 8H.ply │ ├── 8J.ply │ ├── 8K.ply │ ├── 8L.ply │ ├── 9A.ply │ ├── 9B.ply │ ├── 9C.ply │ ├── 9D.ply │ ├── 9E.ply │ ├── 9F.ply │ ├── 9G.ply │ ├── 9H.ply │ ├── 9J.ply │ ├── 9Ka.ply │ ├── 9Kb.ply │ └── 9L.ply ├── integration ├── mC-ATAC │ ├── 01a.prepare_mc.ipynb │ ├── 01b.prepare_atac.ipynb │ ├── 02.merge_and_lsi.ipynb │ ├── 03.integration.ipynb │ ├── 04.embedding.ipynb │ ├── 05.confusion_matrix.use_co_cluster.ipynb │ └── plot.ipynb └── mC-RNA │ ├── README.md │ ├── Snakefile │ └── notebooks │ ├── 01a.select_mc_cef.ipynb │ ├── 01b.select_rna_cef.ipynb │ ├── 02a.prepare_mc.ipynb │ ├── 02b.prepare_rna.ipynb │ ├── 03.merge_and_pca.ipynb │ ├── 04.integration.ipynb │ ├── 05.embedding.ipynb │ └── 06.confusion_matrix.ipynb ├── mapping_pipeline ├── README.md ├── mapping_env.yaml ├── snm3C_example │ ├── Snakefile │ ├── fastq │ │ ├── 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