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mantispy

  • Tutorials
    • 0. Overview: the whole workflow on one page
    • 1. From CellProfiler to AnnData
    • Reading profiles
    • Reading plates
    • 2. From cells to profiles
    • 3. Trustworthy profiles
    • 4. Correcting and evaluating
    • 5. Hits and effects
    • 6. Mechanism of action
    • 7. Single-cell heterogeneity
    • 8. Trustworthy features and experimental design
    • 9. Scaling up, and correcting across laboratories
    • 10. Differential features
  • API
    • mantispy.io.read_profiles
    • mantispy.io.read_plate
    • mantispy.io.read_jump
    • mantispy.io.read
    • mantispy.io.write
    • mantispy.io.validate
    • mantispy.pp.annotate_controls
    • mantispy.pp.annotate_jump
    • mantispy.pp.find_perturbation_key
    • mantispy.pp.calculate_qc_metrics
    • mantispy.pp.filter_cells
    • mantispy.pp.filter_features
    • mantispy.pp.normalize
    • mantispy.pp.feature_select
    • mantispy.pp.subset_features
    • mantispy.pp.outliers
    • mantispy.pp.image_qc
    • mantispy.pp.filter_images
    • mantispy.pp.well_qc
    • mantispy.pp.standardize_feature_names
    • mantispy.pp.sphere
    • mantispy.pp.correct_plate_position
    • mantispy.pp.regress_out
    • mantispy.pp.harmony
    • mantispy.pp.rank_int
    • mantispy.pp.downsample
    • mantispy.pp.feature_select_chatterjee
    • mantispy.pp.feature_reproducibility
    • mantispy.pp.feature_batch_sensitivity
    • mantispy.tl.aggregate
    • mantispy.tl.map
    • mantispy.tl.similarity
    • mantispy.tl.percent_replicating
    • mantispy.tl.grit
    • mantispy.tl.consensus
    • mantispy.tl.effect_size
    • mantispy.tl.wasserstein_features
    • mantispy.tl.differential_features
    • mantispy.tl.feature_signature
    • mantispy.tl.hit_calling
    • mantispy.tl.edistance
    • mantispy.tl.transport
    • mantispy.tl.dose_response
    • mantispy.tl.nn_moa_classify
    • mantispy.tl.moa_enrichment
    • mantispy.tl.feature_sets
    • mantispy.tl.enrich
    • mantispy.tl.rank_features
    • mantispy.tl.rank_sets
    • mantispy.tl.cluster_composition
    • mantispy.tl.subpopulation_hits
    • mantispy.tl.cell_cycle_phase
    • mantispy.tl.neighbors_local_density
    • mantispy.tl.replicate_saturation
    • mantispy.tl.cytotoxicity
    • mantispy.tl.gene_sets
    • mantispy.tl.pathway_coherence
    • mantispy.tl.enrich_hits
    • mantispy.metrics.silhouette_label
    • mantispy.metrics.silhouette_batch
    • mantispy.metrics.lisi
    • mantispy.metrics.pc_regression
    • mantispy.metrics.batch_variance_explained
    • mantispy.metrics.evaluate_correction
    • mantispy.metrics.diagnose_testing
    • mantispy.get.features
    • mantispy.get.to_dataframe
    • mantispy.get.controls
    • mantispy.get.obs_df
    • mantispy.get.var_df
    • mantispy.pl.plate
    • mantispy.pl.cell_counts
    • mantispy.pl.feature_distributions
    • mantispy.pl.nan_matrix
    • mantispy.pl.qc
    • mantispy.pl.plate_effects
    • mantispy.pl.image_qc
    • mantispy.pl.control_drift
    • mantispy.pl.outliers
    • mantispy.pl.feature_correlation
    • mantispy.pl.feature_groups
    • mantispy.pl.feature_signature
    • mantispy.pl.map
    • mantispy.pl.replicate_correlation
    • mantispy.pl.hits
    • mantispy.pl.effect_sizes
    • mantispy.pl.feature_volcano
    • mantispy.pl.dose_response
    • mantispy.pl.moa_confusion
    • mantispy.pl.moa_enrichment
    • mantispy.pl.distance_heatmap
    • mantispy.pl.setting_agreement
    • mantispy.pl.transport
    • mantispy.pl.sets_heatmap
    • mantispy.pl.cluster_composition
    • mantispy.pl.cell_cycle
    • mantispy.pl.density
    • mantispy.pl.subpopulation_hits
    • mantispy.pl.replicate_saturation
    • mantispy.pl.cytotoxicity
    • mantispy.pl.pathway_coherence
    • mantispy.pl.batch_variance
    • mantispy.pl.metrics
    • mantispy.pl.similarity
    • mantispy.ds.synthetic_plate
    • mantispy.ds.blobs
    • mantispy.ds.bbbc021
    • mantispy.ds.rohban
    • mantispy.ds.pki
    • mantispy.ds.jump_target2
    • mantispy.ds.agnp
    • mantispy.ds.amish
    • mantispy.ds.chroma
    • mantispy.ds.jump_crispr
    • mantispy.ds.luad
    • mantispy.ds.miami
    • mantispy.ds.neuropainting
    • mantispy.ds.oasis_pilot
    • mantispy.ds.pooled_rare
    • mantispy.settings
    • mantispy.settings.override
    • mantispy.settings.reset
  • Changelog
  • Contributing guide
  • References

All modules for which code is available

  • mantispy._core.schema
  • mantispy.ds._blobs
  • mantispy.ds._datasets
  • mantispy.ds._synthetic
  • mantispy.get._accessors
  • mantispy.io._jump
  • mantispy.io._plate
  • mantispy.io._profiles
  • mantispy.metrics._diagnose
  • mantispy.metrics._evaluate
  • mantispy.metrics._lisi
  • mantispy.metrics._silhouette
  • mantispy.metrics._variance
  • mantispy.pl._diagnostics
  • mantispy.pl._evaluation
  • mantispy.pl._features
  • mantispy.pl._heterogeneity
  • mantispy.pl._hits
  • mantispy.pl._moa
  • mantispy.pl._plate
  • mantispy.pl._qc
  • mantispy.pl._signature
  • mantispy.pl._transport
  • mantispy.pp._annotate
  • mantispy.pp._batch
  • mantispy.pp._chatterjee
  • mantispy.pp._feature_qc
  • mantispy.pp._image_qc
  • mantispy.pp._names
  • mantispy.pp._normalize
  • mantispy.pp._outliers
  • mantispy.pp._qc
  • mantispy.pp._sample
  • mantispy.pp._select
  • mantispy.pp._sphere
  • mantispy.pp._transform
  • mantispy.pp._well_qc
  • mantispy.tl._aggregate
  • mantispy.tl._consensus
  • mantispy.tl._design
  • mantispy.tl._differential
  • mantispy.tl._distance
  • mantispy.tl._dose
  • mantispy.tl._effect
  • mantispy.tl._enrich
  • mantispy.tl._heterogeneity
  • mantispy.tl._hits
  • mantispy.tl._knowledge
  • mantispy.tl._map
  • mantispy.tl._moa
  • mantispy.tl._signature
  • mantispy.tl._similarity
  • mantispy.tl._transport
  • scanpy.get.get

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