Index

A

adata_count (class in scanpy_plus.magics)

assign_sex() (in module scanpy_plus.pp.assign_sex)

C

calc_pca_dist() (scanpy_plus.tl.map_to_dahlin.Project_landscape method) cellbender() (in module scanpy_plus.pp.cellbender) cellcycle_corr() (in module scanpy_plus.pp.cellcycle_corr)

clean_genes() (in module scanpy_plus.tl.run_scvi) cluster_assignment() (scanpy_plus.tl.map_to_dahlin.Project_landscape method) cmagic() (scanpy_plus.magics.adata_count method)

D

describe() (in module scanpy_plus.describe)

download_cc() (in module scanpy_plus.tl.run_scvi)

G

get_from_raw() (in module scanpy_plus.get_from_raw) get_results() (scanpy_plus.tl.gsea.Gsea method)

getdb() (scanpy_plus.tl.gsea.Gsea method) Gsea (class in scanpy_plus.tl.gsea)

H

histplot() (in module scanpy_plus.pl.histplot)

I

is_outlier() (in module scanpy_plus.is_outlier)

L

labelling() (scanpy_plus.tl.map_to_dahlin.Project_landscape method) lcmagic() (scanpy_plus.magics.adata_count method) lmagic() (scanpy_plus.magics.adata_count method)

load_ipython_extension() (in module scanpy_plus.magics) load_skin() (in module scanpy_plus.data.load) log() (scanpy_plus.tl.map_to_dahlin.Project_landscape method)

M

map_to_dahlin() (in module scanpy_plus.tl.map_to_dahlin) module scanpy_plus scanpy_plus.data scanpy_plus.data.load scanpy_plus.describe scanpy_plus.get_from_raw scanpy_plus.globimport scanpy_plus.io scanpy_plus.io.adata_split scanpy_plus.io.boot scanpy_plus.is_outlier scanpy_plus.magics scanpy_plus.pl scanpy_plus.pl.histplot scanpy_plus.pl.pca_correlation scanpy_plus.pl.perma_plot scanpy_plus.pl.plotly_umap scanpy_plus.pl.ridgeplot scanpy_plus.pl.splitplot scanpy_plus.pl.splitscatter scanpy_plus.pl.umap3dPlotting scanpy_plus.pl.umap_allobs scanpy_plus.pl.umap_grid scanpy_plus.pl.umap_markers scanpy_plus.pp scanpy_plus.pp.assign_sex scanpy_plus.pp.cellbender scanpy_plus.pp.cellcycle_corr scanpy_plus.tl scanpy_plus.tl.gsea scanpy_plus.tl.map_to_dahlin scanpy_plus.tl.rankobs scanpy_plus.tl.run_scvi scanpy_plus.tl.tryumap

N

normalise() (scanpy_plus.tl.map_to_dahlin.Project_landscape method)

P

pca_correlation() (in module scanpy_plus.pl.pca_correlation) pca_project_myadata() (scanpy_plus.tl.map_to_dahlin.Project_landscape method) perma_plot() (in module scanpy_plus.pl.perma_plot) plot_on_ref() (scanpy_plus.tl.map_to_dahlin.Project_landscape method)

plotly_umap() (in module scanpy_plus.pl.plotly_umap) Project_landscape (class in scanpy_plus.tl.map_to_dahlin) pull() (in module scanpy_plus.io.boot) push() (in module scanpy_plus.io.boot)

R

rankobs() (in module scanpy_plus.tl.rankobs) read_adata_split() (in module scanpy_plus.io.adata_split) ridgeplot() (in module scanpy_plus.pl.ridgeplot)

run_gsea() (scanpy_plus.tl.gsea.Gsea method) run_pca_ref() (scanpy_plus.tl.map_to_dahlin.Project_landscape method) run_scvi() (in module scanpy_plus.tl.run_scvi)

S

scale_separately() (scanpy_plus.tl.map_to_dahlin.Project_landscape method) scale_together() (scanpy_plus.tl.map_to_dahlin.Project_landscape method) scanpy_plus module scanpy_plus.data module scanpy_plus.data.load module scanpy_plus.describe module scanpy_plus.get_from_raw module scanpy_plus.globimport module scanpy_plus.io module scanpy_plus.io.adata_split module scanpy_plus.io.boot module scanpy_plus.is_outlier module scanpy_plus.magics module scanpy_plus.pl module scanpy_plus.pl.histplot module scanpy_plus.pl.pca_correlation module scanpy_plus.pl.perma_plot module scanpy_plus.pl.plotly_umap module scanpy_plus.pl.ridgeplot module

scanpy_plus.pl.splitplot module scanpy_plus.pl.splitscatter module scanpy_plus.pl.umap3dPlotting module scanpy_plus.pl.umap_allobs module scanpy_plus.pl.umap_grid module scanpy_plus.pl.umap_markers module scanpy_plus.pp module scanpy_plus.pp.assign_sex module scanpy_plus.pp.cellbender module scanpy_plus.pp.cellcycle_corr module scanpy_plus.tl module scanpy_plus.tl.gsea module scanpy_plus.tl.map_to_dahlin module scanpy_plus.tl.rankobs module scanpy_plus.tl.run_scvi module scanpy_plus.tl.tryumap module scvi_plot() (in module scanpy_plus.tl.run_scvi) splitplot() (in module scanpy_plus.pl.splitplot) splitscatter() (in module scanpy_plus.pl.splitscatter)

T

tryumap() (in module scanpy_plus.tl.tryumap)

U

umap3dPlotting() (in module scanpy_plus.pl.umap3dPlotting) umap_allobs() (in module scanpy_plus.pl.umap_allobs)

umap_grid() (in module scanpy_plus.pl.umap_grid) umap_markers() (in module scanpy_plus.pl.umap_markers)

W

write_adata_split() (in module scanpy_plus.io.adata_split)