satijalab / seurat

R toolkit for single cell genomics

http://www.satijalab.org/seurat

Repository from Github https://github.comsatijalab/seurat

satijalab/seurat Issues

Issue with FindAllMarkers: "Multiple UMI assays are used for SCTransform" after integration in Seurat v5
Updated 14 days ago
LoadVizgen error
Updated 14 days ago4
Read10X() unnecessary slow as it requires Matrix::readMM()
Updated 14 days ago6
Reorder seurat object
Updated 14 days ago1
BUG: IntegrateLayers error on SCTransform and RPCA
Closed 14 days ago4
Is ScaleData by layer?
Closed 15 days ago3
Cell type classification with or without reference integration?
Closed 14 days ago1
How are peaks merged when merging several multiome objects?
Updated 14 days ago
Documentation: Hnsw nearest neighbor method is implemented but not documented
Updated 15 days ago
Different results by running clustering steps (FindNeighbors+FindClusters+RunUMAP) before/after Harmony
Closed 18 days ago3
Normalisation / SCTransform for SVG spatial analysis
Updated 16 days ago2
Documentation: Spatial mouse anterior vignette subset error
Updated 18 days ago
Use IntegrateLayers() or IntegrateData()?
Updated 18 days ago
Instructions on Vignettes, "merged_obj[["RNA"]] <- JoinLayers(merged_obj)" is wrong
Updated 18 days ago
BUG: FindVariableFeatures didnt work on my PCs
Updated 18 days ago1
Unable to reproduce results from seurat vignette
Closed 18 days ago4
Integration single-cell data with spatial transcriptomic from 10x Visium
Closed 18 days ago1
SCTransform generates memory error with a large dataset
Closed 21 days ago6
Integrating multiple Visium HD samples
Closed 18 days ago2
Featureplot works but Dotplot does not
Updated 18 days ago1
Subclustering of SCTransformed Integrated dataset
Closed 18 days ago2
Single cell- feature plots and dot plots
Updated 18 days ago1
Colour gradient legend for integrated dot plot
Closed 18 days ago1
erro in test dataset in LoadAkoya
Closed 18 days ago1
SCT `data` or `scale.data` to select top highly expressed genes in scRNAseq to compare with VST-transformed values in bulkRNAseq?
Closed 18 days ago1
SketchData: Error in Calculating Leverage Score, fails with "NA/NaN/Inf in qr() function" error
Updated 18 days ago1
Documentation: <insert-descriptive-title>:vignettes>description mistake
Updated 18 days ago
SpatialDimPlot() with interactive = T doesn't work for slideseq due to ScaleFactors error
Closed 18 days ago2
Can Seurat v5 integrate Multiome (scRNA-seq+scATAC-seq) and snmC-seq via scMT-seq as the bridge?
Updated 19 days ago
Feature Request: Vignettes section issue
Updated 20 days ago
Updates to UMAP/uwot function
Updated 21 days ago
Error in updating Seurat packages
Closed 21 days ago3
scTransform a multilayered v5 assay is joining the layers in the sct assay, is this correct?
Updated 21 days ago
BUG: cannot open URL - Issues with "satijalab/azimuth", Seurat additional package installation
Updated 21 days ago1
Integrate multiple sample
Closed 22 days ago2
Issue: ScaleData Not Working with BPCells
Updated 25 days ago9
Difficulty using Read10x and CreateSeuratObject
Closed 25 days ago
P-values of NaN or NA from FindMarkers() will crash the FindConservedMarkers() function
Updated a month ago
Feature Request: Please update VlnPlot for better raster points
Updated a month ago2
FindClusters always resulting in 1000+ clusters regardless of resolution
Closed a month ago
FeaturePlot scale changes when put 3 cols
Updated a month ago1
Add `raster.dpi`as parameter for `VlnPlot`
Updated 2 months ago2
Default branch change affecting `remotes::install_github`
Updated 2 months ago
Plotting Clusters on Tissue
Updated 2 months ago
FindAllmarkers => Doheatmap => Heterogeneous clusters
Updated 2 months ago
Analysis of raw counts changes across Seurat versions.
Closed 2 months ago2
Error when projecting reference dataset with on-disc data matrix: "Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 't': Argument 'x' must be of type logical, integer or numeric, not 'list'"
Updated 2 months ago
Visium HD Analysis Vignette Question
Updated 2 months ago8
AggregateExpression on CITEseq protein data
Updated 2 months ago
integration RPCA selecting layer
Updated 2 months ago