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mantispy
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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
11. Concentration response
Datasets
Overview
BBBC021
JUMP-Target-2
Single cells of BR00121438
OASIS pilot
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.jump_cells
mantispy.ds.jump_export
mantispy.ds.jump_plate
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
System Settings
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