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.gitignore
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.Rproj.user
.Rhistory
.RData
.Ruserdata
code/enrichment_analysis/project_all/score/snRNAseq_aggregated_cpm.tsv
code/spot_deconvo/cell2location/02_registration_HE_broad_class.log
code/spot_deconvo/cell2location/02_registration_HE_layer.log
plots/02_build_spe/ReferenceMapping.pdf
plots/02_build_spe/ReferenceMapping_erik.pdf
plots/02_build_spe/prearrangedAllSamples.pdf
plots/02_build_spe/prearrangedSamples.pdf
plots/02_build_spe/rearrangedAllSamples.pdf
plots/02_build_spe/rearrangedSamples.pdf
plots/02_build_spe/rearrangedTransformedAllSamples.pdf
plots/02_build_spe/rearrangedTransformedSamples.pdf
plots/02_build_spe/referenceMapping.pdf
plots/02_build_spe/referenceMapping_allSamples.pdf
plots/04_QC/QC_Br6522.pdf
plots/04_QC/QC_discard_highMito_by_brain.pdf
plots/04_QC/QC_discard_highMito_by_brain_allSamples.pdf
plots/04_QC/QC_discard_highMito_by_capture_area.pdf
plots/04_QC/QC_discard_highMito_by_capture_area_allSamples.pdf
plots/04_QC/QC_discard_lowFeaturesCount_by_brain.pdf
plots/04_QC/QC_discard_lowFeaturesCount_by_brain_allSamples.pdf
plots/04_QC/QC_discard_lowFeaturesCount_by_brain_grid.pdf
plots/04_QC/QC_discard_lowFeaturesCount_by_brain_grid_allSamples.pdf
plots/04_QC/QC_discard_lowFeaturesCount_by_capture_area.pdf
plots/04_QC/QC_discard_lowFeaturesCount_by_capture_area_allSamples.pdf
plots/04_QC/QC_discard_lowFeaturesCount_by_capture_area_grid.pdf
plots/04_QC/QC_discard_lowFeaturesCount_by_capture_area_grid_allSamples.pdf
plots/04_QC/QC_outliers_brain.pdf
plots/04_QC/QC_outliers_brain_allSamples.pdf
plots/04_QC/QC_outliers_capture_area.pdf
plots/04_QC/QC_outliers_capture_area_allSamples.pdf
plots/05_preprocess_batchCorrection/OSCApreprocess_brain_UMAP.pdf
plots/05_preprocess_batchCorrection/OSCApreprocess_brain_UMAP_harmony.pdf
plots/05_preprocess_batchCorrection/OSCApreprocess_captureArea_UMAP.pdf
plots/05_preprocess_batchCorrection/OSCApreprocess_captureArea_UMAP_allSamples.pdf
plots/05_preprocess_batchCorrection/OSCApreprocess_captureArea_UMAP_harmony.pdf
plots/05_preprocess_batchCorrection/OSCApreprocess_captureArea_UMAP_harmony_allSamples.pdf
plots/05_preprocess_batchCorrection/hpc_UMAP_postHarmony.pdf
plots/05_preprocess_batchCorrection/hpc_UMAP_preHarmony.pdf
plots/05_preprocess_batchCorrection/scran_modelGeneVar_captureArea.pdf
plots/05_preprocess_batchCorrection/scran_modelGeneVar_captureArea_allSamples.pdf
plots/05_preprocess_batchCorrection/spatialPreprocess_UMAP.pdf
plots/05_preprocess_batchCorrection/spatialPreprocess_UMAP_harmony.pdf
plots/06_clustering/BayesSpace/1st_run/BayesSpace_harmony_k15_nrep10000.pdf
plots/06_clustering/BayesSpace/1st_run/BayesSpace_rerun_K15_mCluster.pdf
plots/06_clustering/BayesSpace/1st_run/BayesSpace_rerun_K15_spatialCluster.pdf
plots/06_clustering/BayesSpace/1st_run/BayesSpace_rerun_k17_mbkmeans.pdf
plots/06_clustering/BayesSpace/1st_run/BayesSpace_rerun_k17_mbkmeans_mCluster.pdf
plots/06_clustering/BayesSpace/1st_run/BayesSpace_rerun_k17_mbkmeans_mclust.pdf
plots/06_clustering/BayesSpace/1st_run/QCchecks_BayesSpaceK11/BayesSpace_clusters_K11.pdf
plots/06_clustering/BayesSpace/1st_run/QCchecks_BayesSpaceK11/MPPED1_CA1.pdf
plots/06_clustering/BayesSpace/1st_run/QCchecks_BayesSpaceK11/NECAB1_DG+CA3.pdf
plots/06_clustering/BayesSpace/1st_run/QCchecks_BayesSpaceK11/PROX1_DG.pdf
plots/06_clustering/BayesSpace/1st_run/QCchecks_BayesSpaceK11/SLC17A6_subiculum.pdf
plots/06_clustering/BayesSpace/1st_run/QCchecks_BayesSpaceK11/brains.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_k12.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_k13.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_k14.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_k15.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_k16.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_k17.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_k18.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_k20.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_k21.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_k23.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_k24.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_k25.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_k27.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_sample_k18.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_sample_k20.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_sample_k25.pdf
plots/06_clustering/PRECAST/HE_VSPG_PRECAST_sample_k30.pdf
plots/06_clustering/PRECAST/HK_PRECAST_k18.pdf
plots/06_clustering/PRECAST/PC2vsPC1.pdf
plots/06_clustering/PRECAST/PC2vsPC1_wCP.pdf
plots/06_clustering/PRECAST/PC2vsPC1_woCP.pdf
plots/06_clustering/PRECAST/Test_PRECAST_k15.pdf
plots/06_clustering/PRECAST/nnSVG_PRECAST_4k16.pdf
plots/06_clustering/PRECAST/nnSVG_PRECAST_4k17.pdf
plots/06_clustering/PRECAST/nnSVG_PRECAST_k16.pdf
plots/06_clustering/PRECAST/nnSVG_PRECAST_k17.pdf
plots/06_clustering/PRECAST/nnSVG_PRECAST_k18.pdf
plots/06_clustering/PRECAST/nnSVG_PRECAST_k19.pdf
plots/06_clustering/PRECAST/nnSVG_PRECAST_k20.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans17_smoothed.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans17_withlabels.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_10.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_11.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_12.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_13.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_14.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_15.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_16.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_17.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_18.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_19.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_20.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_21.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_22.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_23.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_24.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_25.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_26.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_27.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_28.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_29.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_30.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_5.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_6.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_7.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_8.pdf
plots/06_clustering/mbkmeans/1st_run/mbkmeans_9.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans10.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans11.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans12.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans13.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans14.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans15.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans16.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans17.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans18.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans19.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans20.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans21.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans22.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans23.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans24.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans25.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans26.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans27.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans28.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans29.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans30.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans5.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans6.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans7.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans8.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_brain_mbkmeans9.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans10.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans11.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans12.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans13.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans14.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans15.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans16.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans17.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans18.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans19.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans20.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans21.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans22.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans23.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans24.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans25.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans26.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans27.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans28.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans29.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans30.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans5.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans6.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans7.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans8.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/OSCApreprocess_harmony_captureArea_mbkmeans9.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/spatialPreprocess_harmony_mbkmeans_10.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/spatialPreprocess_harmony_mbkmeans_11.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/spatialPreprocess_harmony_mbkmeans_12.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/spatialPreprocess_harmony_mbkmeans_13.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/spatialPreprocess_harmony_mbkmeans_14.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/spatialPreprocess_harmony_mbkmeans_15.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/spatialPreprocess_harmony_mbkmeans_16.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/spatialPreprocess_harmony_mbkmeans_17.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/spatialPreprocess_harmony_mbkmeans_18.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/spatialPreprocess_harmony_mbkmeans_19.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/spatialPreprocess_harmony_mbkmeans_20.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/spatialPreprocess_harmony_mbkmeans_21.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/spatialPreprocess_harmony_mbkmeans_22.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/spatialPreprocess_harmony_mbkmeans_23.pdf
plots/06_clustering/mbkmeans/preprocess_harmony/spatialPreprocess_harmony_mbkmeans_24.pdf
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