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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
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.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.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.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.AlignmentDistanceCalculator
scirpy.ir_dist.metrics.FastAlignmentDistanceCalculator
scirpy.ir_dist.metrics.TCRdistDistanceCalculator
Immune receptor (IR) model
Glossary
Contributing guide
Changelog
Other versions
Bibliography
.rst
.pdf
Tutorials
Tutorials
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Contents:
Importing receptor data into scirpy
Analysis of 3k T cells from cancer
