Skip to main content
Ctrl+K
mTopic 1.1 documentation - Home mTopic 1.1 documentation - Home

Documentation

  • Installation Guide
  • Tutorial 1: Data Preparation
  • Tutorial 2: Spatial P22 Mouse Brain (ATAC + RNA)
  • Tutorial 3: Spatial Human Tonsil (RNA + Protein Epitopes)
  • Tutorial 4: Single-cell Human PBMC (ATAC + RNA + Protein Epitopes)
  • Tutorial 5: Selecting the number of topics
  • API
    • mtopic.read.h5mu
    • mtopic.pp.permute
    • mtopic.pp.tfidf
    • mtopic.pp.clr
    • mtopic.pp.scale_counts
    • mtopic.pp.filter_var_knee
    • mtopic.pp.filter_var_list
    • mtopic.pp.feature_associations_data
    • mtopic.tl.MTM
    • mtopic.tl.MTM_GPU
    • mtopic.tl.sMTM
    • mtopic.tl.sMTM_GPU
    • mtopic.tl.export_params
    • mtopic.tl.zscores
    • mtopic.tl.umap
    • mtopic.tl.feature_associations
    • mtopic.tl.select_n_topics
    • mtopic.pl.select_n_topics
    • mtopic.pl.filter_var_knee
    • mtopic.pl.filter_topics
    • mtopic.pl.topics
    • mtopic.pl.scatter_pie
    • mtopic.pl.dominant_topics
    • mtopic.pl.signatures
    • mtopic.pl.zscores
    • mtopic.pl.corr_heatmap
    • mtopic.pl.feature_activity

Index

_ | C | D | E | F | H | M | P | S | T | U | V | Z

_

  • __init__() (mtopic.tl.MTM method)
    • (mtopic.tl.MTM_GPU method)
    • (mtopic.tl.sMTM method)
    • (mtopic.tl.sMTM_GPU method)

C

  • clr() (in module mtopic.pp)
  • corr_heatmap() (in module mtopic.pl)

D

  • dominant_topics() (in module mtopic.pl)

E

  • export_params() (in module mtopic.tl)

F

  • feature_activity() (in module mtopic.pl)
  • feature_associations() (in module mtopic.tl)
  • feature_associations_data() (in module mtopic.pp)
  • filter_topics() (in module mtopic.pl)
  • filter_var_knee() (in module mtopic.pl)
    • (in module mtopic.pp)
  • filter_var_list() (in module mtopic.pp)

H

  • h5mu() (in module mtopic.read)

M

  • MTM (class in mtopic.tl)
  • MTM_GPU (class in mtopic.tl)

P

  • permute() (in module mtopic.pp)

S

  • scale_counts() (in module mtopic.pp)
  • scatter_pie() (in module mtopic.pl)
  • select_n_topics() (in module mtopic.pl)
    • (in module mtopic.tl)
  • signatures() (in module mtopic.pl)
  • sMTM (class in mtopic.tl)
  • sMTM_GPU (class in mtopic.tl)
  • SVI() (mtopic.tl.MTM method)
    • (mtopic.tl.MTM_GPU method)

T

  • tfidf() (in module mtopic.pp)
  • topics() (in module mtopic.pl)

U

  • umap() (in module mtopic.tl)

V

  • VI() (mtopic.tl.MTM method)
    • (mtopic.tl.MTM_GPU method)
    • (mtopic.tl.sMTM method)
    • (mtopic.tl.sMTM_GPU method)

Z

  • zscores() (in module mtopic.pl)
    • (in module mtopic.tl)

By Piotr Rutkowski

© Copyright 2026, Piotr Rutkowski.