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Documentation: FindTransferAnchors with an integrated reference - what reduction to use?

documentationError in documentationError in documentation

Status: Open.

#10235 In satijalab/seurat;

· agreco92 opened on Dec 9, 2025

latest umap-learn 0.5.9.post2 crashing version control in RunUMAP

bugSomething isn't workingSomething isn't working

Status: Open.

#10233 In satijalab/seurat;

· daniel-spies opened on Dec 9, 2025

BUG: Projecting SCTransformed + Harmony Integrated Data results in scrambled UMAP

bugSomething isn't workingSomething isn't working

Status: Open.

#10232 In satijalab/seurat;

· tpham2654 opened on Dec 8, 2025

The UMAP positions of the cells inconsistent with their label transfer results.

Status: Open.

#10224 In satijalab/seurat;

· Nickluas opened on Nov 25, 2025

Troubleshooting dotplot error: Error in <code>.rowNamesDF&lt;-</code>(x, value = value) : duplicate 'row.names' are not allowed

Status: Open.

#10222 In satijalab/seurat;

· cancerCoder03 opened on Nov 24, 2025

Error in <code>translate_shape_string()</code>: ! Shape aesthetic contains invalid values: 19.

Status: Open.

#10201 In satijalab/seurat;

· ltzyl opened on Nov 11, 2025

High Time and Memory Consumption of FindIntegrationAnchors Function in Seurat v4 for (500K cells and 2915 genes)

Status: Open.

#10200 In satijalab/seurat;

· Sudhanva1712 opened on Nov 10, 2025

Solution (temp) for plot <code>deparse(substitute(e2, env = caller_env(2))) : 'S4SXP'</code> error

Status: Open.

#10188 In satijalab/seurat;

· anashen opened on Nov 5, 2025

Which Assay to Use for Mapping and Annotation of Query Datasets

Status: Open.

#10187 In satijalab/seurat;

· antsmer opened on Nov 3, 2025

The SCTransform workflow is not compatible with scVIIntegration

bugSomething isn't workingSomething isn't working

Status: Open.

#10184 In satijalab/seurat;

· ZCLZCLZ opened on Nov 3, 2025

BUG: Error in RunCCA.Seurat(object1 = reference, object2 = query, features = features, : VariableFeatures not computed for the SCT assay in object1

bugSomething isn't workingSomething isn't working

Status: Open.

#10165 In satijalab/seurat;

· kangjiajinlong opened on Oct 27, 2025

Regression: <code>ReadXenium</code> does no longer apply transcript QV filtering

bugSomething isn't workingSomething isn't working

Status: Open.

#10155 In satijalab/seurat;

· ppm1337 opened on Oct 23, 2025