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  • Data structure and usage principles
  • Tutorials
    • Importing receptor data into scirpy
      • scirpy.io.read_10x_vdj
      • scirpy.io.read_tracer
      • scirpy.io.read_bracer
      • scirpy.io.read_airr
      • scirpy.io.read_bd_rhapsody
      • scirpy.io.from_dandelion
      • scirpy.io.AirrCell
      • scirpy.io.from_airr_cells
    • Analysis of 3k T cells from cancer
    • BCR analysis in Scirpy
    • Working with >1M cells
  • API
    • scirpy.io.upgrade_schema
    • scirpy.io.read_h5mu
    • scirpy.io.read_h5ad
    • scirpy.io.read_10x_vdj
    • scirpy.io.read_tracer
    • scirpy.io.read_bracer
    • scirpy.io.read_bd_rhapsody
    • scirpy.io.read_airr
    • scirpy.io.from_dandelion
    • scirpy.io.write_airr
    • scirpy.io.to_dandelion
    • scirpy.io.AirrCell
    • scirpy.io.from_airr_cells
    • scirpy.io.to_airr_cells
    • scirpy.pp.index_chains
    • scirpy.pp.merge_airr
    • scirpy.pp.ir_dist
    • scirpy.get.airr
    • scirpy.get.obs_context
    • scirpy.get.airr_context
    • scirpy.tl.group_abundance
    • scirpy.tl.chain_qc
    • scirpy.tl.define_clonotypes
    • scirpy.tl.define_clonotype_clusters
    • scirpy.tl.clonotype_convergence
    • scirpy.tl.clonotype_network
    • scirpy.tl.clonotype_network_igraph
    • scirpy.tl.clonal_expansion
    • scirpy.tl.summarize_clonal_expansion
    • scirpy.tl.alpha_diversity
    • scirpy.tl.repertoire_overlap
    • scirpy.tl.clonotype_modularity
    • scirpy.tl.clonotype_imbalance
    • scirpy.tl.ir_query
    • scirpy.tl.ir_query_annotate
    • scirpy.tl.ir_query_annotate_df
    • scirpy.tl.spectratype
    • scirpy.tl.mutational_load
    • scirpy.pl.embedding
    • scirpy.pl.alpha_diversity
    • scirpy.pl.clonal_expansion
    • scirpy.pl.group_abundance
    • scirpy.pl.spectratype
    • scirpy.pl.vdj_usage
    • scirpy.pl.repertoire_overlap
    • scirpy.pl.clonotype_modularity
    • scirpy.pl.clonotype_network
    • scirpy.pl.clonotype_imbalance
    • scirpy.pl.logoplot_cdr3_motif
    • scirpy.pl.base.bar
    • scirpy.pl.base.line
    • scirpy.pl.base.barh
    • scirpy.pl.base.curve
    • scirpy.pl.styling.apply_style_to_axes
    • scirpy.pl.styling.style_axes
    • scirpy.datasets.wu2020
    • scirpy.datasets.wu2020_3k
    • scirpy.datasets.maynard2020
    • scirpy.datasets.stephenson2021_5k
    • scirpy.datasets.iggytop
    • scirpy.datasets.vdjdb
    • scirpy.datasets.iedb
    • scirpy.util.DataHandler
    • scirpy.util.graph.layout_components
    • scirpy.util.graph.layout_fr_size_aware
    • scirpy.util.graph.igraph_from_sparse_matrix
    • scirpy.ir_dist.sequence_dist
    • scirpy.ir_dist.metrics.DistanceCalculator
    • scirpy.ir_dist.metrics.ParallelDistanceCalculator
    • scirpy.ir_dist.metrics.IdentityDistanceCalculator
    • scirpy.ir_dist.metrics.LevenshteinDistanceCalculator
    • scirpy.ir_dist.metrics.HammingDistanceCalculator
    • scirpy.ir_dist.metrics.GPUHammingDistanceCalculator
    • scirpy.ir_dist.metrics.AlignmentDistanceCalculator
    • scirpy.ir_dist.metrics.FastAlignmentDistanceCalculator
    • scirpy.ir_dist.metrics.TCRdistDistanceCalculator
  • Immune receptor (IR) model
  • Glossary
  • Contributing guide
  • Changelog
  • Other versions
  • Bibliography
  • .rst

Tutorials

Tutorials#

Contents:

  • Importing receptor data into scirpy
  • Analysis of 3k T cells from cancer
  • BCR analysis in Scirpy
  • Working with >1M cells

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Data structure and usage principles

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Importing receptor data into scirpy

By Gregor Sturm, Tamas Szabo

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