├── .Rbuildignore ├── .gitignore ├── CONTRIBUTION ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── CCA_wrappers.r ├── QC_wrappers.r └── update.r ├── README.md ├── man ├── calculatePatchSeqQCMetrics2.Rd ├── compareClusterCalls.Rd ├── defineClassMarkers.Rd ├── qcPlot.Rd ├── reorder_matrix.Rd ├── summarySE.Rd └── update_patchseqtools.Rd ├── manuscript_data ├── .gitkeep ├── Figure3Supplement4_umapdata.csv ├── Figure3Supplement4_violinsdata.csv ├── Figure4A-heatmapdata-Pvalb-IRES-Cre.csv ├── Figure4A-heatmapdata-Rbp4-Cre_KL100.csv ├── Figure4A-heatmapdata-Sst-IRES-Cre.csv ├── Figure4A-heatmapdata-Vip-IRES-Cre.csv ├── Figure4B-heatmapdata.csv ├── Figure4C-maxmappingprobabilitytosinglecluster.csv ├── Figure4Supplement1-heatmapdata-FACS.csv ├── Figure4Supplement1-heatmapdata-nmsfail.csv ├── Figure4Supplement1-heatmapdata-nmspass.csv ├── Figure5C-scatterdata.csv ├── Patchseq_QC_for_methods_paper.Rmd ├── Patchseq_QC_for_methods_paper.nb.html ├── class_markers.csv ├── 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