Discussions

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  Run cell2location with multiple Visium slides or one at a time

  kuang-da asked Jul 21, 2023 in Q&A · Closed · Answered

  

  

  

  

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  Is it possible to train the model with multiple GPU?

  AtlasMaroc asked Nov 8, 2025 in Q&A · Unanswered

  

  

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  Best practice for calculating gene signature scores from cell2location deconvolved layers

  LauraRabade asked Oct 20, 2025 in Q&A · Unanswered

  

  

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  Please use https://discourse.scverse.org/c/ecosytem/cell2location/42 instead

  vitkl asked Dec 10, 2020 in General · Unanswered

  

  

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  Pre-release: normalisation model, plot improvements, bug fixes

  vitkl asked Aug 23, 2021 in Q&A · Unanswered

  

  

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  Preprocessing of scRNA reference

  livyring asked Aug 1, 2022 in Q&A · Unanswered

  

  

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  Choosing one N_cells_per_location for multiple samples

  question Further information is requested

  ThomasThaewel asked Feb 9, 2023 in General · Unanswered

  

  

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  What is the input for signature matrix calculation?

  RolantusdataExp asked Feb 23, 2024 in Q&A · Unanswered

  

  

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  Fitting snRNA-seq to spatial seq

  Jiayi-Zheng asked Nov 15, 2023 in Q&A · Unanswered

  

  

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  LocationModelLinearDependentW model in the new cell2location version

  sokratiag asked Oct 30, 2023 in General · Unanswered

  

  

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  Regarding the modeling details in the paper

  chrissymkcn asked Oct 16, 2023 in General · Unanswered

  

  

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  Deconvolution after bleeding correction

  parkjooyoung99 asked Jun 7, 2023 in Q&A · Unanswered

  

  

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  Scale in plot_genes_per_cell_type

  ChristinaSteyn asked Mar 25, 2023 in Q&A · Unanswered

  

  

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  Plot_spatial Multiple Cell Types Interpretation

  meaksu asked Mar 27, 2023 in Q&A · Unanswered

  

  

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  Confirming values in the cell2location object are cell type abundances

  ChristinaSteyn asked Mar 6, 2023 in Q&A · Unanswered

  

  

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  Difference in spatial mapping methods between tutorials

  meaksu asked Mar 17, 2023 in Q&A · Answered

  

  

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  celltype SC-ST mapping

  enhancement New feature or request

  JingGuo1997 asked Mar 17, 2023 in Q&A · Unanswered

  

  

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  why w_s,f follow gamma distribution

  question Further information is requested

  caiquanyou asked May 25, 2022 in General · Unanswered

  

  

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  Evaluating model like in the first tutorial

  question Further information is requested

  HugoCroizer asked Feb 10, 2022 in Q&A · Unanswered

  

  

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  q05_cell_abundance_w_sf represents the relative abundance of mRNA counts?

  Nasrine26 asked Jan 18, 2022 in Q&A · Answered

  

  

  

  

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  Is it correct to pick the most abundance cell type?

  Jaimomar99 asked Feb 27, 2023 in Q&A · Unanswered

  

  

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  Comparing against cell2location results

  amanda-sun asked Feb 27, 2023 in Q&A · Unanswered

  

  

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  Cell2location reads raw counts as normalized values

  question Further information is requested FAQ

  deconvolute asked Feb 9, 2023 in General · Unanswered

  

  

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  cell2location underestimated cell types density and variability in Visium FFPE samples

  PietroAndrei asked Feb 7, 2023 in Q&A · Unanswered

  

  

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  Error running 'Estimate cell-type specific expression of every gene in the spatial data (needed for NCEM)'

  question Further information is requested FAQ

  ChristinaSteyn asked Feb 6, 2023 in Q&A · Answered

  

  

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