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General
Installation
API
Datasets
mantispy.ds.bbbc021
mantispy.ds.rohban
mantispy.ds.pki
mantispy.ds.jump_target2
mantispy.ds.jump_crispr
mantispy.ds.jump_lite
mantispy.ds.chroma
mantispy.ds.neuropainting
mantispy.ds.oasis_pilot
mantispy.ds.pooled_rare
mantispy.ds.jump_cells
mantispy.ds.jump_export
mantispy.ds.jump_plate
mantispy.ds.scallops_arv471
mantispy.ds.cp_posh
mantispy.ds.corum
mantispy.ds.gene_sets
mantispy.ds.interactions
mantispy.ds.jump_lite_targets
mantispy.ds.synthetic_plate
mantispy.ds.blobs
Overview
BBBC021
Rohban ORF pathway screen
Kinase inhibitors over a dose range
JUMP-Target-2
JUMP CRISPR arm
JUMP-Lite
Chroma
Neuronal Cell Painting
OASIS pilot
Pooled rare variants
Single cells of BR00121438
One CellProfiler export
The images behind one well
SCALLOPS ARV-471
insitro cp-POSH
Reading and writing
mantispy.io.read_profiles
mantispy.io.read_plate
mantispy.io.read_jump
mantispy.io.unexpressed_genes
mantispy.io.read
mantispy.io.write
mantispy.io.stamp
mantispy.io.validate
Preprocessing
mantispy.pp.annotate_controls
mantispy.pp.annotate_jump
mantispy.pp.find_perturbation_key
mantispy.pp.standardize_feature_names
mantispy.pp.calculate_qc_metrics
mantispy.pp.filter_cells
mantispy.pp.filter_features
mantispy.pp.outliers
mantispy.pp.image_qc
mantispy.pp.filter_images
mantispy.pp.well_qc
mantispy.pp.downsample
mantispy.pp.normalize
mantispy.pp.rank_int
mantispy.pp.feature_select
mantispy.pp.subset_features
mantispy.pp.decorr_threshold_sweep
mantispy.pp.feature_select_chatterjee
mantispy.pp.feature_reproducibility
mantispy.pp.feature_batch_sensitivity
mantispy.pp.sphere
mantispy.pp.tvn
mantispy.pp.correct_plate_position
mantispy.pp.detect_plate_position
mantispy.pp.correct_chromosome_arm
mantispy.pp.regress_out
mantispy.pp.harmony
Tools
mantispy.tl.aggregate
mantispy.tl.consensus
mantispy.tl.map
mantispy.tl.similarity
mantispy.tl.percent_replicating
mantispy.tl.grit
mantispy.tl.transport
mantispy.tl.replicate_saturation
mantispy.tl.hit_calling
mantispy.tl.empirical_fdr
mantispy.tl.guide_activity
mantispy.tl.aggregate_guides
mantispy.tl.edistance
mantispy.tl.effect_size
mantispy.tl.wasserstein_features
mantispy.tl.differential_features
mantispy.tl.feature_signature
mantispy.tl.cytotoxicity
mantispy.tl.dose_response
mantispy.tl.dose_features
mantispy.tl.dose_direction
mantispy.tl.dose_trajectory
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
mantispy.tl.gene_sets
mantispy.tl.ora
mantispy.tl.enrich_hits
mantispy.tl.pathway_coherence
mantispy.tl.network_enrichment
mantispy.tl.cluster_composition
mantispy.tl.subpopulation_hits
mantispy.tl.cell_cycle_phase
mantispy.tl.neighbors_local_density
Plotting
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.map
mantispy.pl.replicate_correlation
mantispy.pl.similarity
mantispy.pl.setting_agreement
mantispy.pl.transport
mantispy.pl.replicate_saturation
mantispy.pl.batch_variance
mantispy.pl.metrics
mantispy.pl.hits
mantispy.pl.effect_sizes
mantispy.pl.feature_volcano
mantispy.pl.feature_signature
mantispy.pl.cytotoxicity
mantispy.pl.dose_response
mantispy.pl.dose_direction
mantispy.pl.moa_confusion
mantispy.pl.moa_enrichment
mantispy.pl.distance_heatmap
mantispy.pl.sets_heatmap
mantispy.pl.dendrogram
mantispy.pl.pathway_coherence
mantispy.pl.cluster_composition
mantispy.pl.cell_cycle
mantispy.pl.density
mantispy.pl.subpopulation_hits
Metrics
mantispy.metrics.known_relationships
mantispy.metrics.evaluate_integration
mantispy.metrics.diagnose_testing
mantispy.metrics.pc_regression
mantispy.metrics.batch_variance_explained
Accessors
mantispy.get.features
mantispy.get.to_dataframe
mantispy.get.controls
mantispy.get.obs_df
mantispy.get.var_df
Settings
mantispy.settings
mantispy.settings.override
mantispy.settings.reset
Changelog
Contributing guide
References
Tutorials
General
Mantispy in ten minutes
Quality control
Normalize, select, aggregate
Plate artifacts and corrections
Is the screen any good?
From a CellProfiler run
Published profiles and JUMP
Bringing your own embedding
Images and segmentations
Which measurements moved
Pitfalls
Pseudoreplication
Compound screens
Hits, effects and cell loss
Mechanism of action
Feature-set enrichment
Concentration response
Genetic screens
Interpreting a screen end to end
Single cells
What the well median hides
Case studies
Case studies
Learned embeddings against CellProfiler
Reproducing across laboratories
CRISPR knockouts
Calling hits against genes that cannot respond
Calling gene hits in a pooled screen
Correcting plate position for hit-calling and profiling
About
About mantispy
Citing mantispy
GitHub
Discourse
Repository
Open issue
.md
.pdf
System Settings
Light
Dark
Genetic screens
Genetic screens
#
Interpreting a screen end to end
