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undirected_scores(sme_ud) produces NULL

Status: Open.

#104 In DeshpandeLab/SpaceMarkers;

· orian116 opened on Jun 29, 2026

Naming convention for SpaceMarkers overlap_scores(sme_obj)

Status: Open.

#103 In DeshpandeLab/SpaceMarkers;

· orian116 opened on Jun 29, 2026

Change Nextflow module to use SpatialExperiment object

Status: Open.

#102 In DeshpandeLab/SpaceMarkers;

· atuldeshpande opened on Jun 10, 2026

calculate_influence error due to NAs introduced for barcodes in VisiumHD post RCTD filtering

Status: Open.

#101 In DeshpandeLab/SpaceMarkers;

· orian116 opened on Jun 1, 2026

Loading Spatial Parameters from AnnData and Seurat

Status: Open.

#100 In DeshpandeLab/SpaceMarkers;

· orian116 opened on Jun 1, 2026

refactor output formats

Status: Open.

#89 In DeshpandeLab/SpaceMarkers;

· dimalvovs opened on Dec 19, 2025

allow underscores in cell names

Status: Open.

#86 In DeshpandeLab/SpaceMarkers;

· dimalvovs opened on Dec 16, 2025

Inherit SpaceMarkers object from SpatialExperiment and add wrapper compatibility functions

enhancementNew feature or requestNew feature or request

Status: Open.

Feature

#85 In DeshpandeLab/SpaceMarkers;

· atuldeshpande opened on Dec 9, 2025

Two different pipelines between undirected and directed SpaceMarkers

Status: Open.

#73 In DeshpandeLab/SpaceMarkers;

· orian116 opened on Sep 12, 2025

Visium HD compatibility issues

Status: Open.

#66 In DeshpandeLab/SpaceMarkers;

· dimalvovs opened on May 2, 2025

Parallel findAllHotspots

Status: Open.

#60 In DeshpandeLab/SpaceMarkers;

· dimalvovs opened on Jan 10, 2025

Match default vignette with paper vignette

Status: Open.

#46 In DeshpandeLab/SpaceMarkers;

· atuldeshpande opened on Nov 1, 2024