Nanostring-Biostats/CosMx-Analysis-Scratch-Space

Issues

• Stitching with Napari-cosmx plugin error

  #107 opened 3 months ago by vmezzano21
  0

• Napari-cosmx save error

  #102 opened 4 months ago by pfren1998
  3

• Custom Stitching of Selected FOVs in the Napari-CosMx Plugin?

  #106 opened 3 months ago by keiven-kun
  2

• Channel color assignments differ between FOVs from make_composite.py script

  #105 opened 3 months ago by hmummey
  6

• merging reference profiles - guidance

  #94 opened 4 months ago by patrickjdanaher
  0

• spatial algorithms zoo - additions

  #99 opened 4 months ago by patrickjdanaher
  0

• typo in fov qc vignette

  #96 opened 5 months ago by patrickjdanaher
  0

• batch effects - analysis strategies

  #92 opened 5 months ago by patrickjdanaher
  1

• DE paper

  #95 opened 5 months ago by patrickjdanaher
  0

• multi-sample analyses - strategies

  #93 opened 5 months ago by patrickjdanaher
  0

• Generate Seurat object from flat files

  #90 opened 5 months ago by crwilliams11
  0

• commentary on normalization approaches

  #49 opened 5 months ago by patrickjdanaher
  1

• add tags to python posts: anndata post isn't tagged with "python"

  #85 opened 5 months ago by patrickjdanaher
  0

• insitucor writeup

  #73 opened 5 months ago by patrickjdanaher
  0

• insitucor custom module

  #84 opened 5 months ago by patrickjdanaher
  0

• Make_composite gets an input/output error

  #83 opened 5 months ago by asmilagswash
  2

• AtoMx custom modules: links / commentary / basics

  #82 opened 6 months ago by patrickjdanaher
  0

• Error rendering image from squidpy post

  #79 opened 6 months ago by eveilyeverafter
  0

• build error with h5ad render

  #78 opened 6 months ago by eveilyeverafter
  2

• Differences between legacy and AtoMx flat files

  #75 opened 6 months ago by eveilyeverafter
  1

• how to incorporate AtoMx into open-source analysis workflows

  #76 opened 6 months ago by patrickjdanaher
  0

• Error and missing functionality when using squidpy on AtoMx 1.3.2 exports

  #69 opened 6 months ago by eveilyeverafter
  0

• Blog post with napari ROI selection

  #37 opened 7 months ago by eveilyeverafter
  0

• Stitching panel unavailable in Napari-0.4.19

  #70 opened 6 months ago by NetGebremedhin
  4

• basic analysis vignette - add DE

  #71 opened 6 months ago by patrickjdanaher
  0

• Update to make-composite.py script

  #68 opened 6 months ago by eveilyeverafter
  0

• Napari basics

  #38 opened 6 months ago by eveilyeverafter
  1

• how-to contribute page

  #20 opened 6 months ago by eveilyeverafter
  0

• GeoMx mask generation for single-cell application

  #63 opened 6 months ago by lidanwu
  0

• Creating composite images

  #60 opened 6 months ago by eveilyeverafter
  0

• create h5ad object for interactive viewer and analysis

  #46 opened 6 months ago by lidanwu
  0

• spatial algorithms zoo

  #1 opened 6 months ago by patrickjdanaher
  0

• could not find fastreseg

  #55 opened 7 months ago by Amelie-TGHN
  2

• topic: advanced cell typing

  #30 opened 7 months ago by patrickjdanaher
  1

• lit review of good methods papers

  #51 opened 7 months ago by patrickjdanaher
  0

• spatialUpdate

  #6 opened 7 months ago by patrickjdanaher
  1

• Creating napari-ready files programmatically

  #40 opened 7 months ago by eveilyeverafter
  0

• Add RSS feed configuration to blog

  #25 opened 7 months ago by eveilyeverafter
  1

• needed: quick post on what to do with negprobes

  #28 opened 8 months ago by patrickjdanaher
  0

• install links not working in R

  #22 opened 8 months ago by grkolar
  1

• README (repo) should match the new wording in the about.qmd

  #24 opened 8 months ago by eveilyeverafter
  0

• add viz layout to fov rearranging tools

  #15 opened 9 months ago by patrickjdanaher
  0

• Package of CosMx utilities

  #14 opened 9 months ago by patrickjdanaher
  0

• Background subtraction

  #10 opened 10 months ago by interactivereport
  1

• visualize the neighborhood of query cells in gallery view

  #2 opened a year ago by lidanwu
  0

• point to documentation on raw data formats

  #4 opened a year ago by patrickjdanaher
  0