rajewsky-lab/novosparc

Issues

• Reference atlas creation

  #63 opened 3 years ago by liliay
  1

• visualizing gene expression in multiple slices or 3D

  #56 opened 3 years ago by shermas
  5

• Values for ref atlas

  #59 opened 3 years ago by shermas
  1

• How to create the tissue.png file

  #62 opened 3 years ago by liliay
  1

• No attribute "io" - Input data import

  #61 opened 3 years ago by Diennguyen8290
  0

• novosparc fails (exit 137, process killed)

  #52 opened 3 years ago by dawe
  5

• getting original cell identities with target space locations

  #57 opened 3 years ago by shermas
  1

• error when running tissue.setup_reconstruction

  #60 opened 3 years ago by shermas
  8

• how can I save a tissue object

  #58 opened 3 years ago by shermas
  1

• importing tiff stack for target space

  #55 opened 3 years ago by shermas
  0

• The global transformation use in de novo reconstruction of Drosophila sc RNA-seq data

  #41 opened 3 years ago by hebeishangjiang
  0

• output problem

  #44 opened 3 years ago by caiquanyou
  3

• novosparc exhausts memory when anndata.X in sparse matrix format (CSC or CSR)

  #54 opened 3 years ago by sztankatt
  0

• Question: Use of novosparc on tumor samples

  #53 opened 3 years ago by ccruizm
  2

• division by zero error 'sinkhorn' optimization

  #50 opened 4 years ago by zoepiran
  0

• Reconstruction with Marker Warning

  #46 opened 4 years ago by Hofphi
  2

• Atlas Matrix Bug

  #43 opened 4 years ago by mjang2000
  8

• How to generate the space information for the reference marker genes

  #38 opened 4 years ago by MinjieHu
  8

• Question about implementation and input data

  #48 opened 4 years ago by s849
  0

• Display of ubiquitous genes

  #47 opened 4 years ago by MalteMederacke
  1

• Update dependencies

  #45 opened 4 years ago by MalteMederacke
  1

• problem with create_target_space_from_image() function

  #13 opened 5 years ago by tramdoan
  5

• Downsampling of locations

  #37 opened 5 years ago by MalteMederacke
  2

• Possibility to extract mapping information of cell to location in geometry?

  #42 opened 4 years ago by Hsu-Che-Wei
  2

• Plot positional confidences

  #39 opened 4 years ago by MalteMederacke
  3

• Can we get the relative distance of all cells?

  #30 opened 4 years ago by YiweiNiu
  3

• Full environment and version

  #29 opened 5 years ago by HichamAffia
  3

• Unable to run sample files

  #27 opened 5 years ago by YvonneChenCS
  2

• nc.rc.setup_for_OT_reconstruction

  #20 opened 5 years ago by Counts-Xin
  1

• Repeatability

  #34 opened 5 years ago by Counts-Xin
  5

• About mouse cerebellum slices data

  #26 opened 5 years ago by tauhidstanford
  0

• /novosparc/plotting/_plotting.py

  #36 opened 5 years ago by WhatAboutMyStar
  2

• Create new spatial markes from ISH images

  #35 opened 5 years ago by MalteMederacke
  2

• import novosparc error

  #32 opened 5 years ago by zhangbaso
  0

• How to plot two or more genes in the same time?

  #31 opened 5 years ago by YiweiNiu
  2

• bdtnp.txt file missing

  #23 opened 5 years ago by HichamAffia
  1

• Installation issues

  #25 opened 5 years ago by ccruizm
  5

• ModuleNotFoundError: No module named 'pysal.explore.esda'

  #28 opened 5 years ago by I-Hao
  2

• How to calculate D(exp, phys)?

  #15 opened 5 years ago by ChengxiangQiu
  1

• The object hold Moran’s score

  #22 opened 5 years ago by I-Hao
  2

• Different grids shapes and spatially informative genes

  #11 opened 5 years ago by arielmadr
  2

• bdtnp.txt

  #18 opened 5 years ago by Counts-Xin
  2

• geometry.txt

  #19 opened 5 years ago by grst
  2

• Can you show us a much more detailful vignette from 10X datasets?

  #10 opened 5 years ago by pangxueyu233
  9

• Files not found

  #16 opened 5 years ago by tauhidstanford
  1

• Fix name of output folder in gene plotting function

  #6 opened 5 years ago by nukappa
  0