labsyspharm/scimap

Issues

• How to address spillover in phenotyping.

  #126 opened 2 months ago by josenimo
  1

• Bug when plotting stacked_barplot

  #127 opened 2 months ago by emir-radkevich
  1

• BrokenProcessPool: A task has failed to un-serialize. Please ensure that the arguments of the function are all picklable.

  #125 opened 3 months ago by rohandavidg
  0

• ValueError expecting 2D array at `sm.pp.rescale()` step

  #120 opened 4 months ago by sobjb7osx2
  3

• ValueError: Expected 2D array, got 1D array instead for rescale after manual gating

  #124 opened 4 months ago by rach-crc
  4

• Building neighborhoods

  #123 opened 4 months ago by andreevg04
  1

• %gui qt did not work and napari window did not pop up

  #121 opened 4 months ago by rach-crc
  4

• CODEX dataset with 200 images

  #119 opened 5 months ago by andreevg04
  4

• spatial_interaction - issues with rare cell type handling

  #117 opened 5 months ago by gesavoigt
  0

• Using SCIMAP with MERFISH or Visium data

  #116 opened 6 months ago by poloarol
  1

• return_data not working for plots

  #115 opened 7 months ago by LukasHats
  1

• spatial interaction z scores

  #113 opened 7 months ago by YuanningEric
  0

• Implicit change in matplotlib parameters while importing scimap

  #111 opened 8 months ago by ConstensouxAlexis
  3

• kernel keep dying

  #112 opened 8 months ago by jianxinwang
  3

• overlapping legend on sm.pl.heatmap when constrained_layout set to True, and default arguments

  #108 opened 8 months ago by emmanuel-contreras
  6

• Inquiry on Handling Imbalanced CODEX Data for Cellular Neighborhood Calculations in Scimap

  #110 opened 8 months ago by Yuchen588
  5

• TypeError: Feature names are only supported if all input features have string names, but your input has ['str', 'str_'] when running sm.tl.spatial_cluster

  #107 opened 9 months ago by emmanuel-contreras
  1

• sm.pp.rescale and sm.tl.phenotype for phenotyping not adhering to user-dfined gates

  #106 opened 9 months ago by LukasHats
  6

• Gating QC plots no longer implemented in scimap.pp.rescale()

  #105 opened 10 months ago by CameronFRWatson
  0

• Package test coverage

  #101 opened 10 months ago by jluethi
  7

• spatial_lda reproducibility

  #102 opened a year ago by batukav
  0

• "command not found: pipx" when setting up development environment

  #99 opened a year ago by kevinyamauchi
  2

• scimap installation got error

  #64 opened 2 years ago by bugie19
  11

• adata.raw.X vs. adata.X

  #83 opened a year ago by josenimo
  1

• Wrong figure in the "Getting Started with Scimap" tutorial

  #74 opened a year ago by ziyuanzhao2000
  1

• Numpy ArrayMemoryError

  #91 opened a year ago by lukezhang-811
  1

• Napari doesnt open and code crashes.

  #93 opened a year ago by andreevg04
  5

• upgrade the latest version

  #97 opened a year ago by yas92
  3

• %gui qt not running (M2)

  #82 opened a year ago by virlyananda
  2

• How do I run the tests?

  #100 opened a year ago by kevinyamauchi
  4

• .vscode in the repo

  #98 opened a year ago by kevinyamauchi
  2

• Bug in PIP INSTALL SCIMAP

  #96 opened a year ago by virlyananda
  21

• np.warnings.filterwarnings('ignore') no longer supported by numpy

  #92 opened a year ago by milesbailey121
  3

• Interpretibility of adata.uns['spatial_interaction']

  #88 opened a year ago by Dillon214
  1

• spatial_lda and recurrent cellular neighborhoods

  #71 opened 2 years ago by batukav
  4

• Napari automatically downsamples image when using sm.pl.gate_finder()

  #79 opened a year ago by MargotCh
  3

• batch samples analysis

  #85 opened a year ago by yas92
  3

• how to export the particular data file about the distance calculation

  #70 opened 2 years ago by sailseem
  1

• Can I gate .qptiff image?

  #72 opened 2 years ago by xyin0918
  1

• not maching gating area with the image

  #73 opened 2 years ago by Elena983
  1

• How can I get the test p value of two groups when comparing the distances between two cell types

  #75 opened 2 years ago by sailseem
  1

• supplying additional groupings

  #41 opened 2 years ago by jamesMo84
  2

• Installation problem on Mac

  #76 opened 2 years ago by anaskach
  0

• mcmicro_to_scimap add a condition to error out if multiple dim CSV files are provided

  #69 opened 2 years ago by pantsm
  0

• umap plotting

  #59 opened 2 years ago by ajitjohnson
  0

• Issues with ComBat feature:

  #49 opened 2 years ago by hegewisch15
  1

• Please provide a version cli flag to get package version

  #46 opened 2 years ago by luiskuhn
  2

• Visualization of a single category when plotting umap (sm.pl.umap)

  #48 opened 2 years ago by tuuliavallius
  0

• 'adata = sm.tl.spatial_distance' runs into ValueError: need at most x handles....

  #44 opened 2 years ago by josenimo
  2

• voronoi diagram supply axis

  #39 opened 2 years ago by jim-bo
  0