scverse/scanpy

Issues

• I have always had a question: do I need to scale my adata before running sc.tl.score_genes?

  #3080 opened 4 days ago by christophechu
  0

• Wrongly ordered DotPlot totals in `scanpy` 1.10.1 with Pandas 1.x

  #3062 opened 18 days ago by rgoya
  3

• AttributeError: 'Ingest' object has no attribute '_pca_use_hvg'

  #3074 opened 12 days ago by siebrenf
  0

• Error in running scrublet

  #3070 opened 14 days ago by dicklim
  1

• Adata.raw gets modified upon log normalization of adata

  #3073 opened 12 days ago by AlejandraRodelaRo
  1

• Only show the genes that have significant statistics

  #3077 opened 7 days ago by ngvananh2508
  0

• AxisError when calculating QC metrics on backed data

  #3004 opened 13 days ago by dn-ra
  1

• error in readwrite.py

  #3071 opened 14 days ago by JonatanSahar
  1

• AttributeError: module 'scanpy.preprocessing' has no attribute 'scrublet'

  #3026 opened 15 days ago by bingy007
  2

• Access to Diffusion Map methods (and other embedding methods) as Scikit-Learn style API

  #3054 opened 20 days ago by jolespin
  2

• Broken Scrublet Test

  #3068 opened 17 days ago by ilan-gold
  0

• Switch away from asv

  #3052 opened 21 days ago by flying-sheep
  1

• sc.get.aggregate summary statistics

  #3063 opened 18 days ago by grst
  0

• Benchmarks: Add all from basic tutorial

  #3012 opened 20 days ago by flying-sheep
  0

• will rank_genes_groups_dotplot support results from filter_rank_genes_groups?

  #3049 opened 21 days ago by Li-ZhiD
  4

• More complete dataset documentation

  #3051 opened 21 days ago by flying-sheep
  2

• Unexplainable sc.pp.highly_variable_genes(subset = True) behavior

  #3027 opened a month ago by jberkh
  1

• sc.tl.leiden with `flavor='igraph'` raises an (ignored by igraph) “ValueError: high is out of bounds for int32”

  #3028 opened a month ago by hl324
  6

• Add a needs triage tag

  #3010 opened a month ago by ivirshup
  0

• Tests fail with pytest 8.1 when a `data` dir exists

  #2993 opened a month ago by ivirshup
  13

• Loophole with using scaled adata for sc.tl.score_genes_cell_cycle

  #3030 opened a month ago by kaushik-roy-physics
  0

• When importing Scanpy 1.9.1, if you're using matplotlib version below 3.7, you might encounter a metaclass error.

  #3029 opened a month ago by 12hsk
  5

• tl.leiden suddenly produces different results

  #2956 opened a month ago by Celine-075
  7

• sc.pl.paga_path error in dimensions of array passed to ax.imshow

  #3025 opened a month ago by AlePur
  0

• Update Preprocessing functions with numba

  #3011 opened a month ago by Intron7
  2

• Different clustering results when setting metrics = "cosine", using callable cosine function and direct cos distance input.

  #3021 opened a month ago by zby3
  0

• Failed violins

  #3005 opened 2 months ago by apodtele
  3

• sc.pp.neighbors(..., knn=True, n_neighbors=k) does not threshold the adjacency

  #3014 opened a month ago by mkarikom
  0

• Benchmarks: Add all from Dask tutorial

  #3013 opened 2 months ago by flying-sheep
  0

• Pass n_iterations argument to scanpy.tl.louvain

  #3007 opened 2 months ago by AlSzmigiel
  0

• Future warning in \preprocessing\_highly_variable_genes.py:226

  #2967 opened 2 months ago by dorzhey
  3

• sc.tl.leiden TypeError: unexpected keyword 'flavor'

  #2981 opened 2 months ago by hl324
  1

• Suggestion to support VisiumHD tissue_position_list files (using parquet files)

  #2982 opened 2 months ago by Rafael-Silva-Oliveira
  2

• Performance: Investigate `pp.scale` with sparse matrices

  #2986 opened 2 months ago by Intron7
  1

• why scale is not in spatial

  #2963 opened 2 months ago by asmlgkj
  12

• `sc.tl.ingest`: `pkg_version` does not work with `anndata==0.10.6`

  #2978 opened 2 months ago by maarten-devries
  12

• leiden alg with igraph flavor causes out of bounds freezing

  #2969 opened 2 months ago by RubenVanEsch
  19

• scale for sparse matrixes and mask

  #2941 opened 2 months ago by Intron7
  0

• add support for Visium HD Spatial Gene Expression data

  #2973 opened 2 months ago by 111-dep
  9

• AssertionError: Don’t call _normalize_index with non-categorical/string names

  #2979 opened 2 months ago by alexlenail
  1

• plots in Rstudio messed up

  #2955 opened 2 months ago by Sirin24
  3

• Dask support for normalize_pearson_residuals, highly_variable_genes(flavor='pearson_residuals')

  #2940 opened 2 months ago by eroell
  0

• Adding format checking for sparse matrix in the function "read_v3_10x_h5"

  #2970 opened 2 months ago by CYQFWang
  0

• Dependency on `legacy-api-wrap` prevents 1.10 conda release

  #2966 opened 2 months ago by ivirshup
  1

• sc.get.aggregate looses values

  #2964 opened 2 months ago by grst
  4

• `pl.rank_genes_groups_violin` should be able to pass `**kwds` to `pl.violin`

  #2954 opened 2 months ago by jpintar
  0

• missing scanpy components

  #2949 opened 2 months ago by zjgt
  2

• NMF

  #2938 opened 2 months ago by ivirshup
  0

• NMF

  #2939 opened 2 months ago by ivirshup
  0

• `calculate_qc_metrics` for `dask`

  #2937 opened 2 months ago by ilan-gold
  0