Issues

• Population inference: testing differences WITHIN a cell type within, and then across, replicates

  dmcable/spacexr#262 · Filter by author berniejmulvey opened on Sep 26, 2026

• Help with Error: object 'rctdSim' not found

  dmcable/spacexr#261 · Filter by author Chrisdoan9 opened on May 11, 2026

• pixel count mismatch

  dmcable/spacexr#260 · Filter by author sunshx-bioinfo opened on Mar 26, 2026

• rctd-py

  dmcable/spacexr#259 · Filter by author p-gueguen opened on Mar 10, 2026
  1

• Where to find class-level scores after passing class_df to create.RCTD?

  dmcable/spacexr#255 · Filter by author tangmindan opened on Dec 19, 2025

• Run RCTD gets stuck

  dmcable/spacexr#254 · Filter by author 827613 opened on Nov 17, 2025
  4

• run.RCTD entered a frozen state using max_cores>1

  dmcable/spacexr#253 · Filter by author lexuziandyu opened on Nov 14, 2025
  2

• Run CSIDE without RCTD

  dmcable/spacexr#252 · Filter by author marsdenl opened on Nov 12, 2025

• Doublet mode weights

  dmcable/spacexr#251 · Filter by author edward130603 opened on Oct 27, 2025

• Error occurred when running in multi-thread mode on the cluster.

  dmcable/spacexr#250 · Filter by author liqingsongplus opened on Oct 22, 2025
  1

• Is the keep_reference in create.RCTD right?

  dmcable/spacexr#247 · Filter by author AdotaLover opened on Oct 10, 2025

• Clarification on DE outputs, population inference, and contrasts in run.CSIDE.replicates

  dmcable/spacexr#245 · Filter by author EmanuelSoda opened on Sep 2, 2025
  1

• python version of RCTD

  dmcable/spacexr#244 · Filter by author asmlgkj opened on Aug 28, 2025
  1

• Interpreting first_class in doublet mode with class_df specified

  dmcable/spacexr#243 · Filter by author YuyanRuan opened on Aug 13, 2025

• interpreting meta-analysis results

  dmcable/spacexr#242 · Filter by author abraham-abin13 opened on Aug 4, 2025

• cannot install RCTD issue with predict_CSIDE

  dmcable/spacexr#241 · Filter by author 532at opened on Aug 4, 2025

• the weight of some first_type is lower than second_type in myRCTD@results$weights_doublet

  dmcable/spacexr#239 · Filter by author 050114dragon opened on Jul 20, 2025
  1

• Pre-Processing: Normalization / SpotClean / scIntegration?

  dmcable/spacexr#237 · Filter by author ghost opened on Jul 2, 2025
  2

• count_cell_types default parameters issue

  dmcable/spacexr#236 · Filter by author leealj opened on Apr 28, 2025
  1

• graph output spot size

  dmcable/spacexr#235 · Filter by author chrkuo opened on Apr 3, 2025
  1

• RCTD reference choice

  dmcable/spacexr#234 · Filter by author Chelsea-yy opened on Mar 10, 2025
  1

• Drop cell type in reference

  dmcable/spacexr#233 · Filter by author GCAT01 opened on Mar 3, 2025
  1

• Is there a function that can directly run CSIDE for non-RCTD objects?

  dmcable/spacexr#232 · Filter by author Santanevrgivup opened on Feb 24, 2025
  2

• Post-Processing Cell Annotation of Doublets

  dmcable/spacexr#231 · Filter by author dblevenson opened on Feb 17, 2025
  4

• get_de_genes: At least 90% of genes do not match between the SpatialRNA and Reference objects.

  dmcable/spacexr#229 · Filter by author nasimbio opened on Jan 29, 2025
  3