navinlabcode/CellTrek

Issues

• Error in rownames(st_data[[st_assay]]@data) : no slot of name "data" for this object of class "Assay5", Possible Seurat v5.0 error

  #39 opened a year ago by tsoruu
  6

• Installation problem

  #43 opened 4 months ago by Svvord
  0

• Using Celltrek on non-matching data ST and SC data.

  #42 opened 7 months ago by Dillon214
  0

• [Question] Is it possible to superimpose a network on spatial image?

  #41 opened 7 months ago by MatteoRiva95
  0

• Errors in CellTrek::traint on example data from README

  #36 opened a year ago by katherine-benjamin
  3

• Error: package or namespace load failed for ‘CellTrek’

  #40 opened 9 months ago by Jia-Shen-1212
  0

• ERROR

  #38 opened a year ago by haitianyisee
  1

• celltrek_vis Error

  #37 opened a year ago by a365485265
  0

• Failed to visualize the ST data, error returns "Error in SpatialPlot(object = object, group.by = group.by, images = images, : Could not find any spatial image information"

  #35 opened a year ago by 14MBD4
  1

• Customized Plot

  #34 opened a year ago by awesomedeer
  0

• Normalization methods

  #33 opened a year ago by awesomedeer
  0

• Request for cell type annotation of mouse kidney and DCIS1 datasets

  #32 opened a year ago by shiy-shiy
  0

• Dealing with spatial data with merged samples

  #31 opened a year ago by Kennyluo4
  0

• Celltrek output to spot and cell mapping

  #30 opened a year ago by smk5g5
  0

• Publicly available Single cell data with ST data

  #27 opened 2 years ago by AteeqMKhaliq
  1

• keep raw data in celltrek object

  #25 opened 2 years ago by kguion1
  1

• selection of Edge cut-off threshold for spatial colocalisation of cells

  #26 opened 2 years ago by pratapstat
  2

• lack of single-cell transcriptome data from the same patient

  #28 opened 2 years ago by ozuoano
  1

• "Celltrek"_Simualtion dataset

  #29 opened 2 years ago by 13198910213
  0

• Simualtion dataset

  #6 opened 3 years ago by hiraksarkar
  2

• celltrek_vis error

  #24 opened 2 years ago by wang0430
  1

• Error while running CellTrek:celltrek function

  #23 opened 2 years ago by pratapstat
  1

• clarification on overall method

  #20 opened 2 years ago by kguion1
  2

• General Questions

  #3 opened 3 years ago by cadyyuheng
  3

• Error: 'DT_boot_mst' is not an exported object from 'namespace:CellTrek'

  #22 opened 2 years ago by kaizen89
  0

• How to keep all the metadata from the seurat traint object after running CellTrek::celltrek()

  #15 opened 2 years ago by AF788
  1

• Question about Supplementary Figure 7e

  #16 opened 2 years ago by Chuang1118
  1

• Error in intI(j, n = x@Dim[2], dn[[2]], give.dn = FALSE) : invalid character indexing

  #18 opened 2 years ago by kguion1
  2

• Assigning all single cells

  #21 opened 2 years ago by cadyyuheng
  1

• Visualization and error in celltrek_vis

  #14 opened 3 years ago by s849
  3

• Utilizing CellChat after CellTrek

  #17 opened 2 years ago by kguion1
  1

• Coembedding shows batch effect

  #12 opened 3 years ago by Laolga
  4

• Error: invalid character indexing

  #19 opened 2 years ago by AteeqMKhaliq
  1

• Some cells are missing from output

  #13 opened 3 years ago by smorabit
  4

• should I subset the scRNA data or the ST data?

  #10 opened 2 years ago by Danyking
  1

• tissue_possitions_lists and images outputs for sample DCIS1 and DCIS2

  #11 opened 3 years ago by ruqianl
  2

• Disorder coordiantes for 10x visium data.

  #9 opened 3 years ago by zhou-ran
  3

• Dimension reduce warning in function celltrek

  #7 opened 3 years ago by parkjooyoung99
  2

• Minimum feature overlap between scRNAseq and spatial method?

  #8 opened 3 years ago by annamath
  1

• Question about "celltrek_vis" results

  #4 opened 3 years ago by ZeroLi-Bio
  2

• error on no scal.factors

  #5 opened 3 years ago by bomacchih
  0

• Error in CellTrek::celltrek step

  #2 opened 3 years ago by RENXI-NUS
  5

• The error of CellTrek

  #1 opened 3 years ago by jincanke
  2