.gitignore
Dockerfile
LICENSE
MANIFEST.in
README.md
env.yaml
pyproject.toml
setup.py
.github/workflows/python-publish.yml
analysis/clustering/mc/01-BasicFeatureFiltering.ipynb
analysis/clustering/mc/02-HighlyVariableFeatureSelection.ipynb
analysis/clustering/mc/03a-GeneratemCHAdata.ipynb
analysis/clustering/mc/03b-GeneratemCGAdata.ipynb
analysis/clustering/mc/04a-PreclusteringAndClusterEnrichedFeatures-mCH.ipynb
analysis/clustering/mc/04b-PreclusteringAndClusterEnrichedFeatures-mCG.ipynb
analysis/clustering/mc/05a-Decomposition-mCH.ipynb
analysis/clustering/mc/05b-Decomposition-mCG.ipynb
analysis/clustering/mc/05c-Embedding.ipynb
analysis/clustering/mc/06-Clustering.ipynb
analysis/clustering/mc/07-Plot.ipynb
analysis/clustering/mc/L1_prepare.ipynb
analysis/clustering/mc/L2_prepare.ipynb
analysis/clustering/mc/L3_prepare.ipynb
analysis/clustering/mc/L4_prepare.ipynb
analysis/clustering/mc/MajorRegion_prepare.ipynb
analysis/clustering/mc/Snakefile
analysis/integration/mc_3c/Summary/01.aggregate_confusion_matrix.ipynb
analysis/integration/mc_3c/Summary/02.plot_confusion_matrix.ipynb
analysis/integration/mc_3c/Summary/03.make_integration_summary.ipynb
analysis/integration/mc_3c/Summary/04.make_gene_plots.ipynb
analysis/integration/mc_3c/Summary/all_integroup.ipynb
analysis/integration/mc_3c/Summary/get_m3c_non_neurons.ipynb
analysis/integration/mc_3c/Template/01.select_mc_cef.ipynb
analysis/integration/mc_3c/Template/02a.prepare_mc.ipynb
analysis/integration/mc_3c/Template/02b.prepare_m3c.ipynb
analysis/integration/mc_3c/Template/03.merge_and_pca.ipynb
analysis/integration/mc_3c/Template/04.integration.ipynb
analysis/integration/mc_3c/Template/05.embedding.ipynb
analysis/integration/mc_3c/Template/06.confusion_matrix.ipynb
analysis/integration/mc_3c/Template/07.select_integration_group.ipynb
analysis/integration/mc_3c/Template/Snakefile
analysis/integration/mc_3c/Template/prepare.ipynb
analysis/integration/mc_atac/Summary/01.aggregate_confusion_matrix.ipynb
analysis/integration/mc_atac/Summary/02.plot_confusion_matrix.ipynb
analysis/integration/mc_atac/Summary/all_integroup.ipynb
analysis/integration/mc_atac/Template/01.prepare_mc.ipynb
analysis/integration/mc_atac/Template/02.prepare_atac.ipynb
analysis/integration/mc_atac/Template/03.merge_and_lsi.ipynb
analysis/integration/mc_atac/Template/04.integration.ipynb
analysis/integration/mc_atac/Template/05.embedding.ipynb
analysis/integration/mc_atac/Template/06.confusion_matrix.ipynb
analysis/integration/mc_atac/Template/07.select_integration_group.ipynb
analysis/integration/mc_atac/Template/Snakefile
analysis/integration/mc_atac/Template/prepare.ipynb
analysis/integration/mc_rna/aibs_smart/Summary/01.aggregate_confusion_matrix.ipynb
analysis/integration/mc_rna/aibs_smart/Summary/02.plot_confusion_matrix.ipynb
analysis/integration/mc_rna/aibs_smart/Summary/03.make_integration_summary.ipynb
analysis/integration/mc_rna/aibs_smart/Summary/04.make_gene_plots.ipynb
analysis/integration/mc_rna/aibs_smart/Summary/all_integroup.ipynb
analysis/integration/mc_rna/aibs_smart/Template/01.select_mc_cef.ipynb
analysis/integration/mc_rna/aibs_smart/Template/02a.prepare_mc.ipynb
analysis/integration/mc_rna/aibs_smart/Template/02b.prepare_rna.ipynb
analysis/integration/mc_rna/aibs_smart/Template/03.merge_and_pca.ipynb
analysis/integration/mc_rna/aibs_smart/Template/04.integration.ipynb
analysis/integration/mc_rna/aibs_smart/Template/05.embedding.ipynb
analysis/integration/mc_rna/aibs_smart/Template/06.confusion_matrix.ipynb
analysis/integration/mc_rna/aibs_smart/Template/07.select_integration_group.ipynb
analysis/integration/mc_rna/aibs_smart/Template/Snakefile
analysis/integration/mc_rna/aibs_smart/Template/prepare.ipynb
analysis/integration/mc_rna/aibs_tenx/Summary/01.aggregate_confusion_matrix.ipynb
analysis/integration/mc_rna/aibs_tenx/Summary/02.plot_confusion_matrix.ipynb
analysis/integration/mc_rna/aibs_tenx/Summary/03.make_integration_summary.ipynb
analysis/integration/mc_rna/aibs_tenx/Summary/04.make_gene_plots.ipynb
analysis/integration/mc_rna/aibs_tenx/Summary/all_integroup.ipynb
analysis/integration/mc_rna/aibs_tenx/Template/01.select_mc_cef.ipynb
analysis/integration/mc_rna/aibs_tenx/Template/02a.prepare_mc.ipynb
analysis/integration/mc_rna/aibs_tenx/Template/02b.prepare_rna.ipynb
analysis/integration/mc_rna/aibs_tenx/Template/03.merge_and_pca.ipynb
analysis/integration/mc_rna/aibs_tenx/Template/04.integration.ipynb
analysis/integration/mc_rna/aibs_tenx/Template/05.embedding.ipynb
analysis/integration/mc_rna/aibs_tenx/Template/06.confusion_matrix.ipynb
analysis/integration/mc_rna/aibs_tenx/Template/07.select_integration_group.ipynb
analysis/integration/mc_rna/aibs_tenx/Template/Snakefile
analysis/integration/mc_rna/aibs_tenx/Template/prepare.ipynb
analysis/integration/mc_rna/broad_tenx/Summary/01.aggregate_confusion_matrix.ipynb
analysis/integration/mc_rna/broad_tenx/Summary/02.plot_confusion_matrix.ipynb
analysis/integration/mc_rna/broad_tenx/Summary/03.make_integration_summary.ipynb
analysis/integration/mc_rna/broad_tenx/Summary/04.make_gene_plots.ipynb
analysis/integration/mc_rna/broad_tenx/Summary/all_integroup.ipynb
analysis/integration/mc_rna/broad_tenx/Template/01.select_mc_cef.ipynb
analysis/integration/mc_rna/broad_tenx/Template/02a.prepare_mc.ipynb
analysis/integration/mc_rna/broad_tenx/Template/02b.prepare_rna.ipynb
analysis/integration/mc_rna/broad_tenx/Template/03.merge_and_pca.ipynb
analysis/integration/mc_rna/broad_tenx/Template/04.integration.ipynb
analysis/integration/mc_rna/broad_tenx/Template/05.embedding.ipynb
analysis/integration/mc_rna/broad_tenx/Template/06.confusion_matrix.ipynb
analysis/integration/mc_rna/broad_tenx/Template/07.select_integration_group.ipynb
analysis/integration/mc_rna/broad_tenx/Template/Snakefile
analysis/integration/mc_rna/broad_tenx/Template/non-neuron_annotation.ipynb
analysis/integration/mc_rna/broad_tenx/Template/prepare.ipynb
analysis/integration/merfish_mc/00.prepare.ipynb
analysis/integration/merfish_mc/01.prepare_adata.ipynb
analysis/integration/merfish_mc/02.merge_and_pca.ipynb
analysis/integration/merfish_mc/03.integration.ipynb
analysis/integration/merfish_mc/04.embedding.ipynb
analysis/integration/merfish_mc/05.plot.ipynb
analysis/integration/merfish_rna/00.prepare.ipynb
analysis/integration/merfish_rna/01.prepare_rna_adata.ipynb
analysis/integration/merfish_rna/02.merge_and_pca.ipynb
analysis/integration/merfish_rna/03.integration.ipynb
analysis/integration/merfish_rna/04.embedding.ipynb
analysis/integration/merfish_rna/05.plot.ipynb
gcp/cloud_batch/cb_snakemake_container.json
gcp/cloud_batch/cloudbatch-snakemake-highcpu.sh
gcp/cloud_batch/cloudbatch-snakemake-highmem.sh
gcp/cloud_batch/dockerfile
gcp/sky/env.yaml
gcp/sky/sky-higlass.yaml
gcp/sky/sky-jupyter-large.yaml
gcp/sky/sky-jupyter-super-large.yaml
gcp/sky/sky-jupyter.yaml
gcp/vm/setup_higlass.sh
gcp/vm/setup_mapping.sh
gcp/vm/setup_wmb_vm.sh
gcp/vm/startup.sh
wmb/__init__.py
wmb/_version.py
wmb/google_sheet.py
wmb/utilities.py
wmb.egg-info/PKG-INFO
wmb.egg-info/SOURCES.txt
wmb.egg-info/dependency_links.txt
wmb.egg-info/requires.txt
wmb.egg-info/top_level.txt
wmb.mindnode/contents.xml
wmb.mindnode/viewState.plist
wmb.mindnode/QuickLook/Preview.jpg
wmb.mindnode/style.mindnodestyle/contents.xml
wmb.mindnode/style.mindnodestyle/metadata.plist
wmb/aibs/__init__.py
wmb/annot/__init__.py
wmb/annot/aibs.py
wmb/annot/annot.py
wmb/annot/broad.py
wmb/annot/cemba.py
wmb/annot/glia.py
wmb/annot/integration.py
wmb/brain_region/__init__.py
wmb/brain_region/ccf_ref.py
wmb/broad/__init__.py
wmb/cemba/__init__.py
wmb/cemba/_atac.py
wmb/cemba/_epi_retro.py
wmb/cemba/_mc_and_m3c.py
wmb/files/AIBS.SMART.CellMetadata.213261.csv.gz
wmb/files/AIBS.SMART.DoubletsID.txt.gz
wmb/files/AIBS.SMART.GeneMap.csv
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wmb/files/AIBS.StructureTree.lib
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wmb/files/AIBS.TENX.GeneMap.csv
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wmb/files/AIBS.TENX.SampleMetadata.816.csv.gz
wmb/files/AIBS_smart_missing_info.txt
wmb/files/AIBS_tenx_missing_info.txt
wmb/files/BICCN.BrainRegionMetadata.csv
wmb/files/BROAD.TENX.DoubletsID.txt.gz
wmb/files/BROAD.TENX.GeneMap.csv
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wmb/files/CEMBA.CellMetadata.snm3C-seq.small.csv.gz
wmb/files/CEMBA.CellMetadata.snmC-seq.small.csv.gz
wmb/files/CEMBA.Liu2021Nature.snmC.metadata.csv.gz
wmb/files/CEMBA.snATAC.ClusterDescription.tsv
wmb/files/CEMBA.snm3C.100KImputedCoolURLs.csv.gz
wmb/files/CEMBA.snm3C.100KRawCoolURLs.csv.gz
wmb/files/CEMBA.snm3C.10KImputedCoolURLs.csv.gz
wmb/files/CEMBA.snm3C.10KRawCoolURLs.csv.gz
wmb/files/CEMBA.snm3C.25KImputedCoolURLs.csv.gz
wmb/files/CEMBA.snm3C.25KRawCoolURLs.csv.gz
wmb/files/CEMBA.snm3C.ALLCPaths.csv.gz
wmb/files/CEMBA.snm3C.ContactPaths.csv.gz
wmb/files/CEMBA.snm3C.DoubletsID.txt.gz
wmb/files/CEMBA.snm3C.mCGALLCPaths.csv.gz
wmb/files/CEMBA.snmC-to-snm3C.L4RegionMap.221110.dict
wmb/files/CEMBA.snmC.ALLCPaths.csv.gz
wmb/files/CEMBA.snmC.DoubletsID.txt.gz
wmb/files/CEMBA.snmC.mCGALLCPaths.csv.gz
wmb/files/__init__.py
wmb/files/_aibs.py
wmb/files/_brain_region.py
wmb/files/_broad.py
wmb/files/_cemba.py
wmb/files/_cemba_epi_retro.py
wmb/files/_integration.py
wmb/files/_ref.py
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wmb/files/palette/AIBS.TENX.Annot.V2.csv
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wmb/genes/__init__.py
wmb/genome/__init__.py
wmb/glia/__init__.py
wmb/integration/__init__.py
wmb/pbn/__init__.py