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General
Installation
API
Datasets
pertpy.data.adamson_2016_pilot
pertpy.data.adamson_2016_upr_epistasis
pertpy.data.adamson_2016_upr_perturb_seq
pertpy.data.aissa_2021
pertpy.data.bhattacherjee
pertpy.data.burczynski_crohn
pertpy.data.chang_2021
pertpy.data.combosciplex
pertpy.data.cinemaot_example
pertpy.data.datlinger_2017
pertpy.data.datlinger_2021
pertpy.data.dialogue_example
pertpy.data.distance_example
pertpy.data.dixit_2016
pertpy.data.dixit_2016_raw
pertpy.data.dong_2023
pertpy.data.frangieh_2021
pertpy.data.frangieh_2021_protein
pertpy.data.frangieh_2021_raw
pertpy.data.frangieh_2021_rna
pertpy.data.gasperini_2019_atscale
pertpy.data.gasperini_2019_highmoi
pertpy.data.gasperini_2019_lowmoi
pertpy.data.gehring_2019
pertpy.data.haber_2017_regions
pertpy.data.hagai_2018
pertpy.data.kang_2018
pertpy.data.mcfarland_2020
pertpy.data.norman_2019
pertpy.data.norman_2019_raw
pertpy.data.papalexi_2021
pertpy.data.replogle_2022_k562_essential
pertpy.data.replogle_2022_k562_gwps
pertpy.data.replogle_2022_rpe1
pertpy.data.sc_sim_augur
pertpy.data.schiebinger_2019_16day
pertpy.data.schiebinger_2019_18day
pertpy.data.schraivogel_2020_tap_screen_chr8
pertpy.data.schraivogel_2020_tap_screen_chr11
pertpy.data.sciplex_gxe1
pertpy.data.sciplex3_raw
pertpy.data.shifrut_2018
pertpy.data.smillie_2019
pertpy.data.srivatsan_2020_sciplex2
pertpy.data.srivatsan_2020_sciplex3
pertpy.data.srivatsan_2020_sciplex4
pertpy.data.stephenson_2021_subsampled
pertpy.data.tasccoda_example
pertpy.data.tian_2019_day7neuron
pertpy.data.tian_2019_ipsc
pertpy.data.tian_2021_crispra
pertpy.data.tian_2021_crispri
pertpy.data.weinreb_2020
pertpy.data.xie_2017
pertpy.data.zhao_2021
pertpy.data.zhang_2021
Preprocessing
pertpy.preprocessing.GuideAssignment
Tools
pertpy.tools.PyDESeq2
pertpy.tools.EdgeR
pertpy.tools.WilcoxonTest
pertpy.tools.TTest
pertpy.tools.PermutationTest
pertpy.tools.Statsmodels
pertpy.tools.Mixscape
pertpy.tools.Milo
pertpy.tools.Sccoda
pertpy.tools.Tasccoda
pertpy.tools.Dialogue
pertpy.tools.Enrichment
pertpy.tools.Distance
pertpy.tools.DistanceTest
pertpy.tools.Augur
pertpy.tools.Scgen
pertpy.tools.Cinemaot
pertpy.tools.MLPClassifierSpace
pertpy.tools.LRClassifierSpace
pertpy.tools.CentroidSpace
pertpy.tools.DBSCANSpace
pertpy.tools.KMeansSpace
pertpy.tools.PseudobulkSpace
Metadata
pertpy.metadata.CellLine
pertpy.metadata.Compound
pertpy.metadata.Moa
pertpy.metadata.Drug
pertpy.metadata.LookUp
Contributing guide
Changelog
References
Gallery
Tutorials
Preprocessing
Guide RNA assignment
Tools
Differential gene expression
Mixscape - analysis of single-cell pooled CRSIPR screen
scCODA - Compositional analysis of labeled single-cell data
scCODA - Modeling options and result analysis
tascCODA - Tree-aggregated compositional analysis
Milo - KNN based differential abundance analysis
DIALOGUE - multi cellular programs
Enrichment
Distance metrics
Distance Tests
Augur - cell type prioritization prediction
CINEMA-OT
scGen - Perturbation response prediction
Perturbation Space
Metadata
Metadata annotation
Ontology mapping
Use cases
Use-case: Exploring genetic interation manifolds
Use-case: Deconvoluting drug responses in cancer cell lines
Use-case: Exploring perturbation effects
About
About Pertpy
Citing pertpy
GitHub
Discourse
.md
.pdf
Preprocessing
Preprocessing
#
Guide RNA assignment
