satijalab seurat issues

satijalab / seurat

R toolkit for single cell genomics

http://www.satijalab.org/seurat

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issues

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JoinLayers Error

#9073 zhoujiaqi704 opened 1 hour ago
0
Conversion from h5ad to Seurat object

#9072 AnnaAntonatouPap opened 6 hours ago
0
How to pass continuous_covariate_keys to scVI integration method within IntegrateLayers?

#9071 greengeckoruns opened 7 hours ago
0
FindMarkers - keep all features

#9070 roanvanscheppingen opened 8 hours ago
0
LoadXenium : Error in `.local()`: ! NA values in coordinates

#9069 savarycl opened 12 hours ago
0
Loading data from UMI counts in flatfile format

#9067 drroya opened 2 days ago
0
Colors not changing with DEenrichRPlot plot

#9066 KatGoldfinch opened 2 days ago
0
MT genes when using ensembl genes

#9065 Flu09 opened 2 days ago
0
VlnPlot error when use seurat V5 assays. Error in if (all(data[, feature] == data[, feature][1])) { : missing value where TRUE/FALSE needed

#9064 wangbenwang123 opened 2 days ago
0
Error in UseMethod(generic = "GetTissueCoordinates", object = object) : no applicable method for 'GetTissueCoordinates' applied to an object of class "VisiumV2"

#9061 jadewu77 opened 3 days ago
1
New Xenium output bundle not compatible with ReadXenium() - no more transcripts.csv.gz

#9060 dpcook opened 4 days ago
0
L2 Normalized embeddings

#9059 danielcgingerich opened 4 days ago
0
Is it possible to generate multi genes plot using Featurecounts

#9058 diyabasu97 closed 5 days ago
1
Error integrating ATAC and scRNA data from different platforms using `FindMultiModalNeighbors` :"Error in dimnames(x) <- dn ..."

#9057 Nh-code opened 5 days ago
0
Downsampling in rPCA integration

#9056 lizchcase opened 5 days ago
0
All grouping variables have 1 value only. Computing across all cells. Error: No cell overlap between new meta data and Seurat object

#9055 Flu09 opened 6 days ago
1
Differences in the re-normalization of a public Seurat Object

#9054 evaesquinas closed 5 days ago
1
why findvaribablefeature give warning with error in merged seurat object before harmony integration

#9052 Rimanpreet1 opened 6 days ago
0
BuildNicheAssay run error.

#9050 KoichiHashikawa closed 6 days ago
1
SpatialFeaturePlot and SpatialDimplot cannot show the expressed dot

#9049 gucascau opened 6 days ago
1
Error in match.arg(arg = value, choices = Assays(object = object)) : 'arg' should be one of “RNA”, “SCT”

#9048 MonkeySylvia opened 6 days ago
0
Fov in Visium data/ BuildNicheAssay

#9047 odunola26 closed 6 days ago
2
Error in loading PBMC dataset for Seurat V5 - Introductory Vignette

#9046 LukeStarWars closed 6 days ago
1
BuildNicheAssay; best practice for optimal usage

#9044 KoichiHashikawa opened 1 week ago
2
Test comment and close with GitHub API

#9043 dcollins15 closed 1 week ago
1
SpatialPlots are taking ages to calculate

#9042 TdzBAS closed 1 week ago
1
Unable to load of sparse data matrices provided by 10X genomics

#9041 HEyuanhang111 closed 1 week ago
1
Unable to generate interactive plot using the seurat object as given in the documentation

#9039 diyabasu97 closed 1 week ago
2
Can't find variable features after merging the seurat objects

#9038 XLS987 opened 1 week ago
1
Calculate image features such as RGB or intensity of Visium HD bins

#9036 sunyumail93 closed 1 week ago
2
Major changes on Xenium v3 output files

#9035 agoan27 opened 1 week ago
1
AddModuleScore do not work for Xenium object

#9034 yxue88 opened 1 week ago
0
Visualizing the spatial plots

#9033 Pedramto89 closed 1 week ago
1
Prevent AddModuleScore() adding numbers to the ends of module names, or add argument to the function to toggle this

#9030 wudustan closed 6 days ago
1
DotPlot: negative average expression on scTransformed object

#9029 sagrikachugh closed 1 week ago
1
Subset cells in Seurat data based on reads and gene expression

#9027 zgb963 closed 1 week ago
3
Cannot load PBMC dataset

#9026 mattmccravy closed 1 week ago
3
CosMx spatial transcriptomics analysis by seurat

#9025 arachuzzz opened 1 week ago
5
split integrated xenium objects

#9024 yxue88 opened 1 week ago
2
IntegrateLayers: Error in UseMethod(generic = "Assays", object = object) : no applicable method for 'Assays' applied to an object of class "NULL"

#9023 changve opened 1 week ago
4
Code no longer produces the same UMAP DimPlot after integration

#9022 ptk1601 closed 1 week ago
3
CreateSeuratObject fails to add metadata

#9021 eblchen closed 1 week ago
1
AverageExpression

#9020 yulchen810 closed 1 week ago
1
Genes missing after SCTransform and integration - how best to set # genes retained

#9018 beazors opened 2 weeks ago
1
Integration with RPCA + SCTransform - reference reduction not present

#9017 lizchcase opened 2 weeks ago
1
Split.by should rasterize all plots

#9016 AmandaK-Lilly opened 2 weeks ago
2
FindVariableFeatures of Sketch-based analysis

#9015 BenxiaHu closed 6 days ago
1
getting back the original count matrix after integration

#9014 Huimin721 closed 1 week ago
1
join layers or not ( contradicting vignettes) standard workflow and sketch

#9013 Flu09 opened 2 weeks ago
1
Add a compatibility layer for `VisiumV1` and `VisiumV2` classes

#9012 ppm1337 closed 5 days ago
2