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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SCTransform assay size

#9506 raygozag opened 1 hour ago
0
Number of cell in SCTramsform()

#9505 Chrisdoan9 opened 1 hour ago
0
how to let SCTransform to use all gene to do scale data ?

#9504 lidd77 opened 7 hours ago
0
How to output DoHeatmap matrix data ?

#9503 lidd77 opened 8 hours ago
0
PrepSCTIntegration Error in scale.data[anchor.features, ] : subscript out of limits

#9502 marika300925 opened 9 hours ago
0
ProjectUMAP results lacks accuracy

#9501 andynkili opened 1 day ago
0
Export log2(TPM/10+1) values from Seurat

#9500 Tina-Siqi opened 1 day ago
0
Requesting Seurat v4.9.9.9060

#9499 Victor21v opened 1 day ago
0
Question about ImageDimPlot function

#9497 lidd77 opened 2 days ago
3
Potential Visual Artifact When Adjusting mols.size in ImageDimPlot

#9496 sallyseullee-0821 opened 2 days ago
0
Error in FindTransferAnchors with SCVI Integrated Reference and Query Dataset

#9495 sallyseullee-0821 opened 2 days ago
0
Comparing IntegrateData() and IntegrateLayers()

#9494 luanamarinho opened 3 days ago
0
Fix DimPlot convenience function logic (#9436)

#9493 rharao opened 4 days ago
0
Error in .subscript.2ary(x, i, j, drop = drop): subscript out of bounds

#9492 zhouliping718828 opened 4 days ago
0
SpatialPlot issue: spot sizes within the slices are inconsistent

#9491 onmyojiyys opened 4 days ago
0
Error using IntegrateLayers()

#9489 sguttr opened 6 days ago
1
Unreliable value when using the future package

#9488 AlbertoFabbri93 opened 6 days ago
0
Error in SketchData() due to variable features

#9487 calafell opened 1 week ago
0
Will executing the PCA and UMAP processes according to the cell type change the shape of the UMAP graph?

#9486 TangBluebird opened 1 week ago
2
Error in SCTransform: Warning message: In size + sum(size_args, na.rm = FALSE) : NAs produced by integer overflow ( Similar to Issue #9316)

#9484 JosephEDuke-Cohan opened 1 week ago
10
Issue in "Error in object[[assay]][] <- grp.cors: object of type 'S4' is not subsettable" as shown in spatial_vignette.Rmd because new Seurat assay required subset method

#9483 joesphbeller opened 1 week ago
0
Strong impact of number of ADT PCs on WNN UMAP?

#9482 erflynn opened 1 week ago
1
FeaturePlot for spatial transcriptomics data does not work

#9481 Yijia-Jiang opened 1 week ago
2
Error in validObject(object = object) : invalid class “Assay5” object: Layers must be two-dimensional objects

#9476 sguttr closed 6 days ago
1
JoinLayers and split() errors

#9475 sguttr closed 1 week ago
1
Problem with LoadXenium (+ self-fix that i need a sanity check on) and advice on labelling sample tissue microarray

#9474 YfCem opened 1 week ago
0
Setting Expression Threshold for Molecule Visualization in ImageDimPlot

#9472 sallyseullee-0821 opened 1 week ago
1
PrepSCTIntegration error: do not start to calculate

#9470 BoTang1 closed 1 week ago
1
Could you please tell me how to use ReadXenium() to load the New 10x Xenium Bundle?_no more "cell_feature_matrix"

#9468 imamura-masaki closed 3 days ago
1
`DietSeurat` doesn't drop layers from objects

#9464 rharao opened 1 week ago
3
Is there a vignette/updated pipeline for Akoya qptiffs?

#9463 salasd opened 1 week ago
0
Incorrect Layer Naming and Barcode Misalignment When Merging Seurat Objects Missing an Assay

#9462 maartenciers opened 2 weeks ago
0
Error in SCTransform: Missing cell.attr Argument When Regressing mitoRatio

#9461 EsToHi closed 6 days ago
1
Error with LoadVizgen in Seurat: Possible Issue with .obj File or Manual Loading Needed?

#9460 drchubos opened 2 weeks ago
1
How do I subset based on RAW counts?

#9459 alexwskh opened 2 weeks ago
5
Merge() increments by 1 instead of using add.cell.ids

#9457 jacobHog closed 2 weeks ago
0
Error: make_cell_attr - log_umi contains NA, NaN, or infinite value in SCTransform

#9456 unikill066 closed 6 days ago
2
SpatialPlot not working as its supposed to

#9455 Aditya-Gautam20 opened 2 weeks ago
8
Seurat V5 integration error: "Error in UseMethod(generic = "Assays", object = object) "

#9454 cherrie-g opened 2 weeks ago
2
The example file does not exist.

#9453 yoyoong opened 2 weeks ago
0
Mismatch in Dotplot of raw counts and normalized data

#9452 Rong-ao closed 6 days ago
1
How to analysis the DEGs between smartseq2 data and 10x data

#9451 Linxiaobuskiy closed 6 days ago
1
Zero score when annotate new visium dataset using a reference

#9450 Chrisdoan9 opened 2 weeks ago
3
Add uwot.approx_pow option to RunUMAP for better reproducibility

#9449 daskelly opened 2 weeks ago
0
Loading Pre-Annotated Regions for Visium Analysis

#9448 abadgerw closed 3 days ago
2
where to get fov parameter value for LoadXenium

#9447 lidd77 closed 3 weeks ago
2
Spatial Transcriptomic analysis tutorial: error when loading data

#9446 RenhaoL closed 2 weeks ago
3
Demultiplexing with hashtag oligos vignette - bad link

#9445 jkelrod97 closed 6 days ago
1
SCTransform + Harmony integration --> FindMarkers issue

#9444 bbmorris1 opened 3 weeks ago
2
Why do FindMarkers DE p-values vary significantly between V4 and V5?

#9443 mauritsunkel opened 3 weeks ago
1