scverse/scanpy-tutorials

Issues

• Trajectory inference tutorial: broken category renaming code

  #135 opened a month ago by TranThiHang97
  2

• Further improvements for the advanced visualisation tutorial

  #62 opened 2 years ago by Hrovatin
  3

• Automate tutorial building in CI

  #79 opened 9 months ago by flying-sheep
  3

• Displayed plot size in tutorials

  #115 opened 4 months ago by Hrovatin
  1

• Scale data in Visium tutorial? #question

  #93 opened 5 months ago by Jieran-S
  1

• pbmc scanpy tutorial reproducibility error in sc.tl.leiden arguments

  #85 opened 7 months ago by Lor-96
  2

• Use sklearn-ann in "alternative knn libraries" tutorial?

  #90 opened 7 months ago by ivirshup
  2

• The dataset of the scanpy workshop day2

  #84 opened 9 months ago by cxy-peter
  0

• (bug): `pbmc3k` tutorial is not reproducible

  #82 opened 9 months ago by ilan-gold
  0

• pearson residue normalization project to tSNE coordinates vs UMAP and the surface outline property?

  #63 opened 2 years ago by brainfo
  0

• I want to translate the document out of Chinese version

  #60 opened 2 years ago by zEpoch
  2

• combining protein and RNA

  #42 opened 9 months ago by vladie0
  1

• typo

  #16 opened 5 years ago by chansigit
  1

• Run tutorial on Google Cloud VM instance

  #40 opened 9 months ago by yinshanfang
  1

• spatial tutorial about np.concatenate

  #33 opened 9 months ago by caiquanyou
  1

• normalize_geometric scanpy version?

  #26 opened 4 years ago by bio-la
  0

• Switch to leiden

  #34 opened 4 years ago by flying-sheep
  3

• Spatial integration tutorial has complicated concatenation expression

  #25 opened 4 years ago by ivirshup
  0

• Cannot reproduce trajectory inference tutorial

  #74 opened a year ago by OXPHOS
  0

• Wrong link? I could not connect the link to download pre-processed h5ad file.

  #66 opened a year ago by id-f
  0

• File not found error

  #45 opened 3 years ago by tht17
  3

• Array in 1-dimension erro

  #28 opened 4 years ago by preetida
  0

• key Error - paga_path

  #36 opened 4 years ago by xlw1207
  0

• key Error - pl.paga_path

  #35 opened 9 months ago by xlw1207
  0

• ImportError: Please install the leiden algorithm: `conda install -c conda-forge leidenalg` or `pip3 install leidenalg`.

  #76 opened a year ago by Aspirinnnn
  1

• Bot to update submodule on main repo when PRs are merged

  #69 opened a year ago by adamgayoso
  1

• Finalize linking strategy (where to host, where to link)

  #64 opened a year ago by adamgayoso
  6

• 3k PBMCs tutorial: neighborhood graph scanpy vs. Seurat

  #72 opened a year ago by p-lombard
  2

• pbmc3k - KeyError: 'base'

  #65 opened a year ago by shachafl
  1

• Use myst-nb admonitions

  #67 opened a year ago by adamgayoso
  1

• Analyzing CITE-seq data contains internal comments

  #41 opened 2 years ago by andreas-wilm
  1

• cell type annotation problem

  #44 opened 2 years ago by ryrl9703
  2

• tutorial_pearson_residuals: why are residuals computed twice?

  #57 opened 2 years ago by alexlenail
  1

• pbmc3k tutorial issue

  #55 opened 2 years ago by juliaryann
  0

• how can I know what marker genes the adata contains directly ?

  #54 opened 2 years ago by yingyuan830
  0

• KeyError: 'rank_genes_groups'

  #47 opened 3 years ago by jwweii
  1

• ipynb that can be run as a single pipeline from start to finish

  #53 opened 3 years ago by sylestiel
  1

• Extract Differentialy Expressed Genes for each group

  #51 opened 3 years ago by ViriatoII
  2

• General questions

  #48 opened 3 years ago by chrismahony
  1

• missing code in Paul15?

  #5 opened 3 years ago by Aja23i6
  1

• Analysis and visualization of spatial transcriptomics data

  #37 opened 4 years ago by lu77777777
  0

• differentially expressed genes

  #30 opened 4 years ago by susanGhaderi
  0

• pbmc3k tutorial does weird stuff at the end

  #21 opened 4 years ago by ivirshup
  1

• Spatial Transcriptomics tutorial

  #10 opened 5 years ago by johnsolk
  3

• pip can't find branch @spatial

  #9 opened 5 years ago by franciscogrisanti
  6

• tutorial example fails, AttributeError: module 'scanpy' has no attribute 'settings'

  #1 opened 6 years ago by fizwit
  1