BodenmillerGroup/cytomapper

Issues

• y axis coordinate

  #94 opened 4 months ago by arcolombo
  5

• loadImages Subscript Error

  #93 opened 5 months ago by DarioS
  6

• compImage function

  #92 opened 8 months ago by SchulzDan
  3

• separate container for 'Expression' colorbar in shiny

  #31 opened 8 months ago by toobiwankenobi
  0

• Switch to snapshot unit testing

  #35 opened 8 months ago by nilseling
  1

• Setting custom breaks in colour parameter

  #69 opened a year ago by MureziCapaul
  0

• no detected spatial_community

  #89 opened a year ago by Elena983
  1

• Strip out CytoImageList

  #64 opened a year ago by nilseling
  0

• BPPARAM + on disk handling on images

  #88 opened a year ago by andrea-de-micheli
  3

• In measureObjects, replace merge by left_join

  #87 opened a year ago by nilseling
  0

• Fix corner case bug in cytomapperShiny

  #85 opened a year ago by nilseling
  0

• Fix pattern argument in loadImages function

  #55 opened a year ago by nilseling
  1

• Cytomappershiny questions

  #78 opened a year ago by ssaintsoon
  2

• Question for scale_bar for images used for publication?

  #77 opened a year ago by Pancreas-Pratik
  2

• Modifying `h5FilesPath` for `CytoImageList` object

  #76 opened 2 years ago by ynanli
  3

• Reader function for single-channel tiffs

  #60 opened 2 years ago by nilseling
  3

• Memory usage with big data sets

  #73 opened 2 years ago by Mark-Ste
  3

• Color legend change

  #75 opened 2 years ago by Tsuyshi
  0

• Bug in violin plot

  #70 opened 2 years ago by nilseling
  1

• Make image handling more efficient

  #58 opened 3 years ago by nilseling
  11

• Developmental changes

  #67 opened 2 years ago by nilseling
  0

• Cytomappershiny - Error: Graphics API version mismatch

  #65 opened 2 years ago by jparkinson375
  9

• Add option to remove cells after gating

  #66 opened 2 years ago by nilseling
  0

• CytomapperShiny gating only applies to one ROI of the 6

  #61 opened 2 years ago by tessbrodie
  6

• mcols to colData

  #62 opened 2 years ago by ellispatrick
  2

• show clustering groups in cytomapper

  #59 opened 3 years ago by sailseem
  3

• Keep metadata when compensating images

  #56 opened 3 years ago by nilseling
  1

• Add function to compensate images

  #53 opened 3 years ago by nilseling
  1

• Missing system libraries on Ubuntu 20.04 for EBImage

  #52 opened 3 years ago by jwindhager
  5

• Allow multiple colour list entries even when colouring only one factor

  #46 opened 3 years ago by nilseling
  1

• Add option to load .h5 files into CytoImageList object

  #49 opened 3 years ago by nilseling
  1

• Allow/document cowplot/patchwork support

  #47 opened 3 years ago by nilseling
  1

• Warinings and errors when reading tif file exported with qupath

  #50 opened 3 years ago by kaizen89
  4

• How to export cell mask from qupath?

  #48 opened 3 years ago by kaizen89
  6

• Bug when setting `legend = NULL`

  #45 opened 4 years ago by nilseling
  1

• Scale function should take multiple scaling factors

  #34 opened 4 years ago by nilseling
  1

• Implement cellDist function

  #44 opened 4 years ago by nilseling
  2

• Implement a measureObjects function

  #38 opened 4 years ago by nilseling
  1

• Implement HDF5Array backend

  #37 opened 4 years ago by nilseling
  1

• Use shinytest for javascript testing

  #36 opened 4 years ago by nilseling
  1

• add option to visualize densities in scatter plots in shiny

  #39 opened 4 years ago by nilseling
  0

• legend with many elements is not fully visible

  #26 opened 4 years ago by toobiwankenobi
  1

• Make return_plot output conform with ggplot/cowplot

  #28 opened 4 years ago by nilseling
  1

• Normalizing individual channels with different inputRanges

  #24 opened 4 years ago by JanaFischer
  2

• extend vignette section 8.1 Subsetting the SingleCellExperiment object

  #25 opened 4 years ago by toobiwankenobi
  1

• Change "highly multiplexed imaging cytometry" to "highly multiplexed imaging" everywhere

  #23 opened 4 years ago by nilseling
  1

• shiny: wrong outlines

  #32 opened 4 years ago by toobiwankenobi
  1

• Test if images that are being returned are numerically the same as EBImage output

  #20 opened 5 years ago by nilseling
  0

• Figure out why subset_images is slower than subsetting the list directly

  #22 opened 5 years ago by nilseling
  1

• Make normalize function more efficient

  #21 opened 5 years ago by nilseling
  1