MarcElosua/SPOTlight

Issues

• Column `abs(coord_y - ymax)` is not found when plotSpatialScatterpie

  #120 opened 18 days ago by xiang-cy
  0

• Can the SPOTlight handle Visium HD data?

  #119 opened a month ago by dfgao
  0

• Error in .filter(x[mod_genes, ], y[mod_genes, ]) : Insufficient number of features shared between single-cell and mixture dataset.

  #118 opened 2 months ago by Angel030331
  0

• Subset Cells in ScatterPie

  #117 opened 6 months ago by ABauer26
  1

• function plotSpatialScatterpie with image=TRUE does not work

  #86 opened 2 years ago by sondvo
  6

• trainNMF error

  #116 opened 8 months ago by Lihyunseo
  7

• HELP! imgData is not equal to the spatialcoords

  #115 opened 9 months ago by GODCALLMEGOD
  0

• Scatterpie

  #114 opened 9 months ago by ljy-sys
  0

• packages version

  #95 opened 9 months ago by caofy0307
  3

• Error in .extract_coord(x = x, slice = slice, img = img) : !is.null(colnames(x)) is not TRUE

  #113 opened 9 months ago by Noralii
  1

• How to annotate a spot as a type of cell

  #112 opened 9 months ago by M-jk22
  1

• assay %in% SeuratObject：：Assays（x） is not TRUE

  #111 opened a year ago by 628511miao
  2

• Deconvolution cannot identify tumor cell type in tumor spatial data

  #71 opened a year ago by hansong798
  2

• Error slot %in% SummarizedExperiment::assayNames(x) is not TRUE

  #85 opened a year ago by williamsdrake
  3

• Questions about some details in paper

  #107 opened a year ago by NianzhenGu
  2

• In README.md the processed object can not find

  #98 opened a year ago by Han117
  2

• dplyr::mutate() Error

  #105 opened a year ago by ABauer26
  2

• plotInteractions

  #87 opened a year ago by wang0430
  8

• Q - Visium analysis - subset image and spot demultiplexing

  #94 opened a year ago by cathalgking
  5

• Error from `.extract_counts()` when calling `SeuratObject::GetAssayData()` v5.0.1

  #110 opened a year ago by WuyangFF95
  1

• Error in `SeuratObject::GetAssayData()`:

  #91 opened 2 years ago by wang0430
  6

• Passing dataframe with NAs into plotCorrelationMatrix

  #109 opened a year ago by arrhenia
  1

• Error in trainNMF(x = x, y = y, groups = groups, mgs = mgs, n_top = n_top, : ids %in% names(mgs) are not TRUE

  #83 opened 2 years ago by BenjaminDEMAILLE
  2

• How to plot specific cell type proportions in the newest version of spotlight?

  #103 opened a year ago by awesomedeer
  1

• Fixed Matrix version incompatible with SeuratObject

  #108 opened a year ago by lardenoije
  1

• downsample_se_obj

  #106 opened a year ago by zhangmin513
  1

• scatter plot circles instead of sctter pie circles

  #100 opened a year ago by cathalgking
  1

• residuals of the sum of squares doesn't work for Seurat object

  #101 opened a year ago by MirDom
  2

• Prepare for upcoming Seurat v5 release

  #102 opened a year ago by saketkc
  0

• plotSpatialScatterpie

  #92 opened 2 years ago by wang0430
  9

• SPOTlight_1.0.0 on Bioconductor .zip cannot be downloaded

  #104 opened a year ago by feasiblee
  0

• Regarding the PBMC (GSE133549) dataset used in the method

  #99 opened a year ago by Han117
  1

• plotInteractions result meaning

  #96 opened 2 years ago by wang0430
  1

• What does the 'decon_df' mean?

  #88 opened 2 years ago by White2album
  5

• Error in .extract_counts(y, assay, slot) : !is.null(colnames(x)) is not TRUE

  #89 opened 2 years ago by carlosccfraga
  2

• assay %in% SeuratObject::Assays(x) is not TRUE

  #93 opened 2 years ago by wang0430
  1

• ST technology (the predecessor of 10X Visium technology)

  #90 opened 2 years ago by wang0430
  1

• Problem on spotlight_deconvolution(old version)

  #73 opened 2 years ago by tewengtong
  1

• Issue plotSpatialScatterpie with a SpatialExperiment object

  #70 opened 2 years ago by Zifeng-L
  3

• SPOTlight function crashes R studio session

  #74 opened 2 years ago by sokratiag
  4

• export SPOTlight results to 10x Genomics Loupe Browser

  #76 opened 2 years ago by sdwien
  3

• colData(sc_data)$subclass

  #77 opened 2 years ago by wang0430
  1

• SPOTlight with low numbers of genes per spot

  #79 opened 2 years ago by sdwien
  1

• ERROR: dependency ‘arrangements’ is not available for package ‘SPOTlight’

  #81 opened 2 years ago by galaxyeee
  4

• Parallel run

  #84 opened 2 years ago by BenjaminDEMAILLE
  2

• test_spot_fun

  #82 opened 2 years ago by umar1196
  2

• Does the new version of SPOTlight no longer support data from Seurat?

  #80 opened 2 years ago by Lukadon77
  1

• Difference between cell type correlation and cell communication

  #78 opened 2 years ago by wang0430
  1

• Convert mgs to data.frame

  #75 opened 2 years ago by nesilin
  1

• Suspected incorrect variable names used in vignette

  #72 opened 2 years ago by Nick-Eagles
  1