lilab-bcb/pegasus

Issues

• how to subplot in pegasus?

  #266 opened 2 months ago by x1han
  2

• counts.log_norm+scale in pegasus vs. scale.data in Seurat and scanpy

  #259 opened 2 months ago by x1han
  3

• Potential Bug in Infer Doublets

  #313 opened 3 months ago by hl-xue
  0

• Buffer dtype mismatch when running de_analysis on AnnData object from scanpy (with testcase)

  #312 opened 3 months ago by hvbakel
  0

• How to Embed BBKNN Results into MultimodalData?

  #311 opened 3 months ago by x1han
  0

• Questions about installation of the version "infercnv"

  #310 opened 4 months ago by Richard-D-Watson
  1

• using cellbender outputs

  #299 opened 5 months ago by jackhump
  2

• Subset using a list of barcodes

  #273 opened a year ago by yoavhadas
  4

• AttributeError: 'UnimodalDataView' object has no attribute '_clean_tmp'

  #147 opened 4 years ago by Zifeng-L
  3

• Inconsistent z-score calculation for CSC and CSR sparse matrices

  #288 opened 8 months ago by jkanche
  4

• Error with FLE

  #265 opened 10 months ago by Zifeng-L
  2

• [ERROR] ValueError: Buffer dtype mismatch, expected 'const float' but got 'unsigned int'

  #280 opened 10 months ago by brauliovaldebenitomaturana
  2

• Error with pegasus.calc_kBET

  #271 opened a year ago by hl-xue
  0

• scTransform support

  #257 opened 2 years ago by mikecuoco
  0

• 【Bug】leiden or louvain clustering error

  #256 opened 2 years ago by Zifeng-L
  6

• on disk reading of a large h5ad file

  #254 opened 2 years ago by hoondy
  0

• How can I plot diffusion map by DC2 and DC3?

  #247 opened 2 years ago by Zifeng-L
  2

• Expose `legend_fontsize` in `scatter` function to users

  #235 opened 2 years ago by yihming
  1

• 1.2.0 L/S method

  #253 opened 2 years ago by Dohyun-s
  1

• Mismatch dtype for diff_expr.py

  #248 opened 2 years ago by tsigalko2003
  0

• pegasus.fgsea NOT work with MOUSE genome

  #243 opened 3 years ago by LNGDingj
  4

• L/S method is deprecated in version 1.4.5?

  #241 opened 3 years ago by niehu2018
  3

• error when using aggregate_matrices to aggregate two multimodaldata

  #236 opened 3 years ago by daisyyr
  1

• clustering based on a subset of cells

  #220 opened 3 years ago by hoondy
  3

• Error reporting when run "pg.fle(data, rep=harmony_key)"

  #226 opened 3 years ago by Zifeng-L
  6

• Cell cycle regress before run_scanorama?

  #227 opened 3 years ago by Zifeng-L
  0

• AttributeError: 'UnimodalData' object has no attribute 'filter_data'

  #179 opened 3 years ago by Zifeng-L
  2

• ValueError: fill value must be in categories

  #156 opened 3 years ago by swemeshy
  2

• qcviolin separated plots?

  #176 opened 3 years ago by YichaoOU
  2

• Is there any academic paper for pegasus?

  #222 opened 3 years ago by tangmaomao16
  1

• Conda yaml for pegasus

  #184 opened 3 years ago by bschilder
  16

• KeyError: 'n_genes'

  #188 opened 3 years ago by bschilder
  4

• Kernel dies during pg.neighbors()

  #185 opened 3 years ago by bschilder
  6

• Seurat? Conditions to channels?

  #183 opened 4 years ago by s849
  1

• Issue while trying to run pegasus_analysis.ipynb

  #182 opened 4 years ago by rgranit
  4

• Error in cell_cycle_calculating

  #124 opened 4 years ago by Zifeng-L
  2

• After loading a 10X h5 PCA does not work

  #89 opened 4 years ago by tariqdaouda
  1

• marker_dict is modified by pg.write_results_to_excel()

  #145 opened 4 years ago by slowkow
  1

• pca() got an unexpected keyword argument 'robust'

  #161 opened 4 years ago by Zifeng-L
  2

• Error with tsne function after following the Regress Out tutorial

  #154 opened 4 years ago by morgeur
  1

• SystemError: bad argument to internal function

  #114 opened 4 years ago by slowkow
  5

• pg.read_input() cannot read an h5 created by pg.write_output()

  #123 opened 4 years ago by slowkow
  2

• Error in pg.mark_doublets

  #112 opened 4 years ago by Zifeng-L
  2

• ValueError: Matrix key 'raw.X' already exists!

  #115 opened 4 years ago by slowkow
  1

• Question about pc_regress_out

  #133 opened 4 years ago by Zifeng-L
  2

• ValueError: Buffer dtype mismatch, expected 'const int' but got 'long'

  #118 opened 4 years ago by slowkow
  3

• "X_" should be "W_"

  #129 opened 4 years ago by slowkow
  1

• ModuleNotFoundError: No module named 'numpy'

  #126 opened 4 years ago by slowkow
  2

• Could you add dendrogram into violinplot?

  #116 opened 4 years ago by Zifeng-L
  0

• After loading an 10X h5 highly variable features does not run

  #90 opened 4 years ago by tariqdaouda
  1