├── .gitignore ├── LICENSE ├── R ├── aggregate_umis_pseudobulks.R ├── cellbrowser_prep.R ├── cellranger_PlotUmiFrequency.R ├── cellranger_plotUmiMitochondrial.R ├── cellranger_plotUmiRank.R ├── cellranger_postprocessAggrMatrix.R ├── cellranger_rawQcMetrics.R ├── cellranger_subsetAndDownsample.R ├── dropest_aggr.R ├── dropest_export_layers.R ├── export_for_python.R ├── fetch_geneset_annotations.R ├── genesetAnalysis.R ├── install.packages.R ├── paga_prepare_input.R ├── plot_group_numbers.R ├── plot_group_numbers_old.R ├── plot_rdims_cluster_genes.R ├── plot_rdims_factor.R ├── plot_rdims_gene.R ├── plot_tsne_hyperparameters.R ├── plot_velocity.R ├── plot_violins.R ├── scanpy_post_process_clusters.R ├── seurat_FindMarkers.R ├── seurat_begin.R ├── seurat_characteriseClusterDEGenes.R ├── seurat_cluster.R ├── seurat_clusterStats.R ├── seurat_cluster_marker_plots.R ├── seurat_clustree.R ├── seurat_compare_clusters.R ├── seurat_compute_dm.R ├── seurat_create_object.R ├── seurat_dm.R ├── seurat_explore_hvg_and_cell_cycle.R ├── seurat_find_neighbors.R ├── seurat_get_assay_data.R ├── seurat_jackstraw.R ├── seurat_normalise_and_scale.R ├── seurat_pca.R ├── seurat_plot_dm.R ├── seurat_summariseMarkerNumbers.R ├── seurat_summariseMarkers.R ├── seurat_summariseMarkersBetween.R ├── seurat_topMarkerHeatmap.R ├── seurat_tsne.R ├── seurat_umap.R ├── singleR_extra_plots.R ├── singleR_plots.R ├── singleR_run.R ├── summariseGenesets.R └── summarise_clusterStats.R ├── README.md ├── Rmd ├── qc_scatterplots.R └── qc_scatterplots.yml ├── docs ├── AlignedExample.md ├── DEPENDENCIES.md └── INSTALL.md ├── latex ├── endmatter.tex └── preamble.sty ├── pipelines ├── pipeline_cellranger.py ├── pipeline_cellranger │ ├── conf.py │ └── pipeline.yml ├── pipeline_scxl.py ├── pipeline_scxl │ ├── beginReport.tex │ ├── clusterMarkerReport.tex │ ├── clusterReport.tex │ ├── clusteringSection.old.tex │ ├── clusteringSection.tex │ ├── clustree.tex │ ├── conf.py │ ├── diffusionSection.tex │ ├── dimensionReductionSection.tex │ ├── geneExpressionReport.tex │ ├── genesetBetweenSection.tex │ ├── genesetSection.tex │ ├── hvgAndCellCycle.tex │ ├── introReport.tex │ ├── introductionSection.tex │ ├── jackstrawSection.tex │ ├── knownmarkersSection.tex │ ├── markerGenes.tex │ ├── markerGenesByCluster.tex │ ├── markerReport.tex │ ├── numbersSection.tex │ ├── pagaSection.tex │ ├── pcaSection.tex │ ├── phateSection.tex │ ├── pipeline.yml │ ├── qcSection.tex │ ├── rdimsVisSection.tex │ ├── ruvSection.tex │ ├── scveloForceDirectedGraphSection.tex │ ├── scveloPhateSection.tex │ ├── scveloSection.tex │ ├── singleRSection.tex │ ├── summaryStatsSection.tex │ ├── taskSummary.tex │ ├── topMarkerHeatmap.tex │ ├── tsneSection.tex │ ├── umapSection.tex │ ├── variableGeneSection.tex │ ├── velocitySection.tex │ └── withinClusterComparisonSection.tex └── pipeline_utils │ ├── TASK.py │ ├── __init__.py │ ├── resources.py │ ├── spec.py │ └── templates.py ├── python ├── ._run_paga.py ├── make_anndata.py ├── requirements.txt ├── run_cluster.py ├── run_paga.py ├── run_phate.py ├── run_scvelo.py ├── run_umap.py └── untitled └── tenxutils ├── DESCRIPTION ├── NAMESPACE ├── R ├── AlluvialPlots.R ├── Cluster.R ├── Helper.R ├── Latex.R ├── Matrix.R ├── Plot.R ├── Seurat.R └── ViolinPlots.R └── man ├── FastExpMeanChunked.Rd ├── Read10X.Rd ├── barcode2table.Rd ├── categoriseGenes.Rd ├── checkCells.Rd ├── checkFeatures.Rd ├── convertHumanGeneList.Rd ├── downsampleMatrix.Rd ├── expressionPlots.Rd ├── expressionPlots3D.Rd ├── g_legend.Rd ├── getCellCycleGenes.Rd ├── getFigureTex.Rd ├── getHVG.Rd ├── getSigPC.Rd ├── getSubFigureTex.Rd ├── getSubsectionTex.Rd ├── getSubsubsectionTex.Rd ├── getViolinData.Rd ├── gg_color_hue.Rd ├── makeViolins.Rd ├── markerComplexHeatmap.Rd ├── plotAlluvial.Rd ├── plotDownsampling.Rd ├── plotFvE.Rd ├── plotGrob.Rd ├── plotHorizontalViolins.Rd ├── plotMA.Rd ├── plotViolins.Rd ├── plotVolcano.Rd ├── readClusterIDs.Rd ├── removeGrobs.Rd ├── save_ggplots.Rd ├── 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