Issues

• We’re removing scanpy.external

  enhancement
  KrishnaswamyLab/PHATE#182 · Filter by author flying-sheep opened on Aug 14, 2026

• Enable out-of-sample projection with precomputed affinities

  enhancement
  Feature

  KrishnaswamyLab/PHATE#181 · Filter by author aumona opened on Jul 1, 2026
  4

• The PHATE Operator get's stuck in the landmark operation when using precomputed knn_dist

  bug
  KrishnaswamyLab/PHATE#175 · Filter by author bjoaofelipe opened on Mar 3, 2026
  2

• Update PHATE documentation

  KrishnaswamyLab/PHATE#173 · Filter by author MattScicluna opened on Jan 26, 2026
  

• PHATE incompatible with NumPy ≥2.0 despite requirement specifying numpy>=1.16.0

  bug
  KrishnaswamyLab/PHATE#169 · Filter by author nishuang83 opened on Oct 25, 2025
  1

• memory requirement for large-ish dataset

  question
  KrishnaswamyLab/PHATE#155 · Filter by author yanlingpan opened on May 30, 2025
  1

• Cannot import PHATE

  KrishnaswamyLab/PHATE#154 · Filter by author mmr181 opened on May 22, 2025
  1

• EBdata used for trajectory inference？

  question
  KrishnaswamyLab/PHATE#150 · Filter by author Han-zh210 opened on Dec 27, 2024

• How does PHATE handle new data?

  question
  KrishnaswamyLab/PHATE#147 · Filter by author wsk-byun opened on Nov 9, 2024

• What is happening in mds.method = "classic"?

  question
  KrishnaswamyLab/PHATE#145 · Filter by author JayaniLakshika opened on Sep 6, 2024

• Providing init to the phateR implementation only saves up time if only the parameter t is changing but not other parameters?

  question
  KrishnaswamyLab/PHATE#143 · Filter by author erzakiev opened on Apr 16, 2024
  1

• Intrinsic dimension of PHATE embedding identifes branches

  question
  KrishnaswamyLab/PHATE#142 · Filter by author YYT1002 opened on Mar 28, 2024

• Support more graphs for phate.fit

  enhancement
  KrishnaswamyLab/PHATE#141 · Filter by author dsm-72 opened on Dec 9, 2023

• Error: TypeError: __init__() got an unexpected keyword argument 'k'

  question
  KrishnaswamyLab/PHATE#140 · Filter by author handesome opened on Sep 22, 2023

• Cannot import phate: numpy version?

  bug
  KrishnaswamyLab/PHATE#136 · Filter by author haoqichen20 opened on Apr 22, 2023
  2

• destination is read-only

  bug
  KrishnaswamyLab/PHATE#134 · Filter by author AndrewSkelton opened on Mar 21, 2023

• Application of PHATE to Visium 10x data

  enhancement
  KrishnaswamyLab/PHATE#133 · Filter by author tyaoi opened on Mar 20, 2023

• cell type annotations of EB

  question
  KrishnaswamyLab/PHATE#128 · Filter by author ShobiStassen opened on Feb 8, 2023
  1

• Recommended minimum number of cells to run PHATE?

  question
  KrishnaswamyLab/PHATE#127 · Filter by author kuang-da opened on Jan 29, 2023

• cell-cycle & mitochondrial regression

  question
  KrishnaswamyLab/PHATE#126 · Filter by author kvshams opened on Jan 4, 2023
  2

• Adding cell id (input rowname) in PHATE output (Y_phate in python tutorial :EmbryoidBody)

  enhancement
  KrishnaswamyLab/PHATE#121 · Filter by author parkjooyoung99 opened on Dec 7, 2022
  1

• Update bioconda

  enhancement
  KrishnaswamyLab/PHATE#120 · Filter by author dsm-72 opened on Nov 10, 2022
  1

• T-PHATE algorithm

  question
  KrishnaswamyLab/PHATE#115 · Filter by author apathanasiadis opened on Jun 6, 2022

• MDS smacof n_jobs argument

  bug
  KrishnaswamyLab/PHATE#112 · Filter by author choltz95 opened on Mar 3, 2022
  1

• SVD computation error message

  bug
  KrishnaswamyLab/PHATE#108 · Filter by author ivan-marroquin opened on Jun 10, 2021