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General

  • Installation
  • API
    • Datasets
      • mantispy.ds.aconcagua
      • 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.depmap_expression
      • 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.from_dataframe
      • 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_set_network
      • 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
      • mantispy.metrics.variance_carried
    • 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
  • Contributing guide
  • References

Data model

  • Data model
  • The mantispy stamp (uns["mantispy"])
  • Schema specification

Tutorials

  • General
    • Mantispy in ten minutes
    • Bring your own data
    • Quality control
    • Normalize, select, aggregate
    • Plate artifacts and corrections
    • Is the screen any good?
    • Choosing a readout
    • 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
    • Optical pooled screens
    • 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
  • Known limitations
  • GitHub
  • Discourse
  • Single cells
  • GitHub
  • Discourse
  • scverse.org
  • Core
  • AnnData
  • decoupler
  • MuData
  • Muon
  • Pertpy
  • rapids-singlecell
  • Scanpy
  • Scirpy
  • scvi-tools
  • SnapATAC2
  • SpatialData
  • Squidpy
  • Ecosystem
  • AESTETIK
  • AlphaPeptTools
  • annbatch
  • anndata for R
  • anndataR
  • annsel
  • AnnZarro
  • ATLAS
  • benGRN
  • bento-tools
  • biolord
  • cell2location
  • Cell_BLAST
  • CellAnnotator
  • CellCharter
  • CellMapper
  • CellOracle
  • CellphoneDB
  • CellRank
  • cellxgene
  • Cirrocumulus
  • clone2vec
  • dandelion
  • delnx
  • DOTools_py
  • DoubletDetection
  • DRVI
  • dvp-io
  • dynamo-release
  • epiScanpy
  • eschr
  • fava
  • flashdeconv
  • flowsom
  • GPTBioInsightor
  • grassp
  • GRnnData
  • gssnng
  • hotspot
  • illico
  • infercnvpy
  • kompot
  • LazySlide
  • liana
  • Marsilea
  • maxspin
  • moscot
  • Mowgli
  • Multivelo
  • ncountr
  • NicheNetPy
  • nichepca
  • novae
  • omicverse
  • Palantir
  • Panpipes
  • ParTIpy
  • PathML
  • pcdl
  • PEAKQC
  • pegasus
  • PILOT
  • popV
  • pycea
  • pychromVAR
  • pyCrossTalkeR
  • PyDESeq2
  • pyLemur
  • pySCENIC
  • pytximport
  • pyUCell
  • Rectangle
  • SC2Spa
  • SCALEX
  • scanpro
  • scCellFie
  • scDataLoader
  • scFates
  • scGen
  • schist
  • scib
  • scib-metrics
  • scib-rapids
  • scmcp
  • scPRINT
  • scPRINT-2
  • scTriangulate
  • scVelo
  • scviva-tools
  • scxmatch
  • scXpand
  • scyan
  • sift-sc
  • sincei
  • Sobolev Alignment
  • sopa
  • spatial-eggplant
  • spatialdataR
  • spatialproteomics
  • spatiomic
  • STMiner
  • Symphonypy
  • tangram
  • TAU Community Detection
  • TreeData
  • vitessce
  • wsidata
  • zellkonverter

Single cells#

  • What the well median hides

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Interpreting a screen end to end

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What the well median hides

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