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  • Installation
  • Tutorials
    • Basics
      • Preprocessing and clustering
      • Preprocessing and clustering 3k PBMCs (legacy workflow)
      • Integrating data using ingest and BBKNN
    • Plotting
      • Core plotting functions
      • Customizing Scanpy plots
    • Trajectories
      • Trajectory inference for hematopoiesis in mouse
    • Experimental
      • How to preprocess UMI count data with analytic Pearson residuals
      • Using dask with Scanpy
  • Usage Principles
  • How to
    • Cell-Cycle Scoring and Regression
    • Using other kNN libraries in Scanpy
    • Plotting with Marsilea
  • API
    • Preprocessing: pp
      • scanpy.pp.calculate_qc_metrics
      • scanpy.pp.filter_cells
      • scanpy.pp.filter_genes
      • scanpy.pp.highly_variable_genes
      • scanpy.pp.log1p
      • scanpy.pp.pca
      • scanpy.pp.normalize_total
      • scanpy.pp.regress_out
      • scanpy.pp.scale
      • scanpy.pp.sample
      • scanpy.pp.downsample_counts
      • scanpy.pp.recipe_zheng17
      • scanpy.pp.recipe_seurat
      • scanpy.pp.combat
      • scanpy.pp.harmony_integrate
      • scanpy.pp.scrublet
      • scanpy.pp.scrublet_simulate_doublets
      • scanpy.pp.hashsolo
      • scanpy.pp.bbknn
      • scanpy.pp.neighbors
    • Tools: tl
      • scanpy.pp.pca
      • scanpy.tl.tsne
      • scanpy.tl.umap
      • scanpy.tl.draw_graph
      • scanpy.tl.diffmap
      • scanpy.tl.embedding_density
      • scanpy.tl.leiden
      • scanpy.tl.dendrogram
      • scanpy.tl.dpt
      • scanpy.tl.paga
      • scanpy.tl.ingest
      • scanpy.tl.rank_genes_groups
      • scanpy.tl.filter_rank_genes_groups
      • scanpy.tl.marker_gene_overlap
      • scanpy.tl.score_genes
      • scanpy.tl.score_genes_cell_cycle
    • Plotting: pl
      • scanpy.pl.scatter
      • scanpy.pl.heatmap
      • scanpy.pl.dotplot
      • scanpy.pl.tracksplot
      • scanpy.pl.violin
      • scanpy.pl.stacked_violin
      • scanpy.pl.matrixplot
      • scanpy.pl.ranking
      • scanpy.pl.dot_area
      • scanpy.pl.clustermap
      • scanpy.pl.dendrogram
      • scanpy.pl.DotPlot
      • scanpy.pl.MatrixPlot
      • scanpy.pl.StackedViolin
      • scanpy.pl.highest_expr_genes
      • scanpy.pl.highly_variable_genes
      • scanpy.pl.scrublet_score_distribution
      • scanpy.pl.pca
      • scanpy.pl.ranking
      • scanpy.pl.pca_loadings
      • scanpy.pl.pca_variance_ratio
      • scanpy.pl.pca_overview
      • scanpy.pl.umap
      • scanpy.pl.tsne
      • scanpy.pl.diffmap
      • scanpy.pl.draw_graph
      • scanpy.pl.embedding_density
      • scanpy.pl.spatial
      • scanpy.pl.embedding
      • scanpy.pl.dpt_groups_pseudotime
      • scanpy.pl.dpt_timeseries
      • scanpy.pl.paga
      • scanpy.pl.paga_path
      • scanpy.pl.paga_compare
      • scanpy.pl.correlation_matrix
      • scanpy.pl.rank_genes_groups
      • scanpy.pl.rank_genes_groups_violin
      • scanpy.pl.rank_genes_groups_stacked_violin
      • scanpy.pl.rank_genes_groups_heatmap
      • scanpy.pl.rank_genes_groups_dotplot
      • scanpy.pl.rank_genes_groups_matrixplot
      • scanpy.pl.rank_genes_groups_tracksplot
    • Reading and Writing
      • scanpy.io.write
      • scanpy.io.read
      • scanpy.io.read_10x_h5
      • scanpy.io.read_10x_mtx
      • scanpy.io.read_h5ad
      • scanpy.io.read_csv
      • scanpy.io.read_excel
      • scanpy.io.read_hdf
      • scanpy.io.read_mtx
      • scanpy.io.read_text
      • scanpy.io.read_umi_tools
    • Get object from AnnData: get
      • scanpy.get.obs_df
      • scanpy.get.var_df
      • scanpy.get.pca
      • scanpy.get.rank_genes_groups_df
      • scanpy.get.aggregate
    • Queries
      • scanpy.queries.biomart_annotations
      • scanpy.queries.mitochondrial_genes
      • scanpy.queries.enrich
    • Metrics
      • scanpy.metrics.modularity
      • scanpy.metrics.confusion_matrix
      • scanpy.metrics.gearys_c
      • scanpy.metrics.morans_i
    • Experimental
      • scanpy.experimental.pp.normalize_pearson_residuals
      • scanpy.experimental.pp.normalize_pearson_residuals_pca
      • scanpy.experimental.pp.highly_variable_genes
      • scanpy.experimental.pp.recipe_pearson_residuals
    • Classes
      • scanpy.Neighbors
    • Settings
      • scanpy.set_figure_params
      • scanpy.settings
      • scanpy.settings.override
      • scanpy.Preset
      • scanpy.Verbosity
      • scanpy.logging.print_header
    • Datasets
      • scanpy.datasets.blobs
      • scanpy.datasets.ebi_expression_atlas
      • scanpy.datasets.krumsiek11
      • scanpy.datasets.moignard15
      • scanpy.datasets.pbmc3k
      • scanpy.datasets.pbmc3k_processed
      • scanpy.datasets.pbmc68k_reduced
      • scanpy.datasets.paul15
      • scanpy.datasets.visium_sge
    • Deprecated functions
      • scanpy.pp.subsample
      • scanpy.pp.recipe_weinreb17
      • scanpy.tl.louvain
      • scanpy.tl.sim
      • scanpy.pl.sim
      • scanpy.queries.gene_coordinates
      • scanpy.datasets.toggleswitch
      • scanpy.logging.print_versions
      • scanpy.read_loom
      • scanpy.read_visium
  • External API
    • Preprocessing: PP
      • scanpy.external.pp.bbknn
      • scanpy.external.pp.mnn_correct
      • scanpy.external.pp.scanorama_integrate
      • scanpy.external.pp.hashsolo
      • scanpy.external.pp.magic
    • Tools: TL
      • scanpy.external.tl.phate
      • scanpy.external.tl.palantir
      • scanpy.external.tl.trimap
      • scanpy.external.tl.sam
      • scanpy.external.tl.phenograph
      • scanpy.external.tl.harmony_timeseries
      • scanpy.external.tl.wishbone
      • scanpy.external.tl.palantir
      • scanpy.external.tl.palantir_results
      • scanpy.external.tl.sandbag
      • scanpy.external.tl.cyclone
    • Plotting: PL
      • scanpy.external.pl.phate
      • scanpy.external.pl.trimap
      • scanpy.external.pl.sam
      • scanpy.external.pl.wishbone_marker_trajectory
    • Exporting
      • scanpy.external.exporting.spring_project
      • scanpy.external.exporting.cellbrowser
  • Release notes
  • Community
  • Contributing
    • Contributing code
    • Getting set up
    • Tests
    • Documentation
    • CI
    • Versioning
    • Making a release
  • Contributors
  • References
  • API
  • Metrics
  • GitHub
  • Discourse
  • scverse.org
  • Core
  • AnnData
  • decoupler
  • MuData
  • Muon
  • Pertpy
  • rapids-singlecell
  • Scanpy
  • Scirpy
  • scvi-tools
  • SnapATAC2
  • SpatialData
  • Squidpy
  • Ecosystem
  • AESTETIK
  • AlphaPeptTools
  • annbatch
  • anndata for R
  • anndataR
  • annsel
  • ATLAS
  • benGRN
  • bento-tools
  • biolord
  • cell2location
  • Cell_BLAST
  • CellAnnotator
  • CellCharter
  • CellMapper
  • CellOracle
  • CellphoneDB
  • CellRank
  • cellxgene
  • Cirrocumulus
  • clone2vec
  • dandelion
  • delnx
  • DOTools_py
  • DoubletDetection
  • DRVI
  • dvp-io
  • dynamo-release
  • epiScanpy
  • eschr
  • fava
  • flashdeconv
  • flowsom
  • GPTBioInsightor
  • grassp
  • GRnnData
  • gssnng
  • hotspot
  • illico
  • infercnvpy
  • kompot
  • LazySlide
  • liana
  • Marsilea
  • maxspin
  • moscot
  • Mowgli
  • Multivelo
  • ncountr
  • NicheNetPy
  • nichepca
  • novae
  • omicverse
  • Palantir
  • Panpipes
  • ParTIpy
  • PathML
  • pcdl
  • PEAKQC
  • pegasus
  • PILOT
  • popV
  • pycea
  • pychromVAR
  • pyCrossTalkeR
  • PyDESeq2
  • pyLemur
  • pySCENIC
  • pytximport
  • pyUCell
  • Rectangle
  • SC2Spa
  • SCALEX
  • scanpro
  • scCellFie
  • scDataLoader
  • scFates
  • scGen
  • schist
  • scib
  • scib-metrics
  • scib-rapids
  • scmcp
  • scPRINT
  • scPRINT-2
  • scTriangulate
  • scVelo
  • scviva-tools
  • scxmatch
  • scXpand
  • scyan
  • sift-sc
  • sincei
  • Sobolev Alignment
  • sopa
  • spatial-eggplant
  • spatialdataR
  • spatialproteomics
  • spatiomic
  • STMiner
  • Symphonypy
  • tangram
  • TAU Community Detection
  • TreeData
  • vitessce
  • wsidata
  • zellkonverter

Metrics#

Collections of useful measurements for evaluating results.

metrics.modularity

Compute the modularity of a graph given its connectivities and labels.

metrics.confusion_matrix

Given an original and new set of labels, create a labelled confusion matrix.

metrics.gearys_c

Calculate Geary's C.

metrics.morans_i

Calculate Moran’s I Global Autocorrelation Statistic.

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scanpy.queries.enrich

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