saezlab/liana-py

Issues

• Proper Caching for MetalinksDB & HCOP

  #111 opened 7 months ago by dbdimitrov
  2

• Using data loader for performing tensor Factorization

  #136 opened 4 months ago by Mona1982
  6

• get_hcop_orthologs

  #137 opened 4 months ago by tuhulab
  1

• CellChat AttributeError: 'SparseCSRView' object has no attribute 'A'

  #135 opened 4 months ago by AmyOlex
  1

• Guidelines to choose the best parameters for bivariate analysis using Visium HD data

  #133 opened 4 months ago by Rafael-Silva-Oliveira
  5

• Support for Calligraphy ?

  #134 opened 4 months ago by divyanshusrivastava
  1

• CCI network map for global LR interactions between cell types

  #132 opened 4 months ago by Rafael-Silva-Oliveira
  5

• Does LIANA+ support Visium HD data?

  #131 opened 5 months ago by Rafael-Silva-Oliveira
  36

• Plot SVGs are massive in size due to color legend

  #129 opened 5 months ago by dnjst
  2

• fail in running https://liana-py.readthedocs.io/en/latest/notebooks/misty.html

  #130 opened 5 months ago by huiyijiangling
  1

• Batch aware filtering of interactions in lrs_to_views

  #128 opened 5 months ago by demian1
  3

• Saving Misty model as .pkl

  #127 opened 5 months ago by Zach-Sten
  3

• Questions about LIANA+ requirement for cell number

  #126 opened 5 months ago by jun-miao113
  3

• ZeroDivisionError: float division by zero

  #93 opened 9 months ago by anke-king
  10

• Metabolite-protein interaction analysis did not show results

  #124 opened 5 months ago by jun-miao113
  5

• pandas name index [BUG]

  #120 opened 5 months ago by dbdimitrov
  0

• Make sure that bivariate throws an exception when nz_prop leads to no genes being considered

  #121 opened 5 months ago by dbdimitrov
  0

• Update MOFAcell Tutorial

  #86 opened 5 months ago by dbdimitrov
  0

• Liana on pseduo bulk-sc data data

  #96 opened 5 months ago by Marwansha
  6

• LR_means, meaning?

  #107 opened 5 months ago by soniyalama
  2

• Bug on Differential Expression Analysis for CCC & Downstream Signalling Networks Vignette

  #117 opened 6 months ago by maximelepetit
  3

• Frequency Chord diagram and Heatmap in Python

  #85 opened a year ago by maximelepetit
  10

• Spatially informed bivariate metrics in tensor cell2cell and MOFA

  #123 opened 6 months ago by Zach-Sten
  3

• Issue with orthologue conversion

  #122 opened 6 months ago by chrika2
  2

• Import Error: Cannot Import name RandomForestModel

  #116 opened 6 months ago by poloarol
  3

• Improve spatial neighbours function

  #112 opened 6 months ago by dbdimitrov
  0

• Clarifications Differential analysis vignette

  #118 opened 6 months ago by maximelepetit
  1

• ValueError: Please check if appropriate organism/ID type was provided!

  #97 opened 6 months ago by anke-king
  6

• MOFA talk with multiple samples

  #101 opened 6 months ago by nicolebussola
  1

• GeneA_GeneB gene expression level error

  #115 opened 7 months ago by alecdavi
  2

• Volcano plots for differentially expressed signaling pairs

  #113 opened 7 months ago by Zach-Sten
  2

• Clarify LIANA + MOFA vignette

  #102 opened 7 months ago by dbdimitrov
  2

• KeyError: None when using top_n parameter in li.pl.dotplot

  #109 opened 7 months ago by WeipengMO
  2

• bandwith in multiple samples

  #106 opened 7 months ago by SopjudeS
  4

• Please check if appropriate organism/ID type was provided! Allowed proportion (0.98) of missing resource elements exceeded (1.00).

  #105 opened 8 months ago by soniyalama
  10

• Sanity check if liana uses the log normalised values

  #104 opened 8 months ago by ahmetrifaioglu
  1

• Add a tutorial on GPU-accelerated misty

  #100 opened 8 months ago by dbdimitrov
  0

• AnnData dtype argument deprecation

  #103 opened 8 months ago by dbdimitrov
  0

• code li.pl.dotplot output an disappointing result

  #95 opened 8 months ago by Fanyu000
  5

• Export Elbow plot from nmf

  #99 opened 8 months ago by dbdimitrov
  0

• Generate Union of Causal Net Predictions

  #82 opened 8 months ago by dbdimitrov
  0

• Add a check that for the subset of cell types in `li.multi.dea_to_lr`

  #92 opened 8 months ago by dbdimitrov
  0

• Flow chart to guide standard LIANA+ workflows

  #94 opened 9 months ago by dbdimitrov
  0

• Getting an error in liana multi df_to_lr

  #84 opened 9 months ago by ndrubins
  15

• Error with li.mt.rank_aggregate.by_sample

  #87 opened 9 months ago by Marwansha
  2

• Question regarding ranking and aggregating from all methods.

  #88 opened 10 months ago by Marwansha
  5

• Magnitude ranks identical in same sample across cell type

  #89 opened 10 months ago by ShadHOH
  2

• Move Vignettes to Another Repo

  #90 opened 10 months ago by dbdimitrov
  0

• move LIANA+ plots to matplotlib and seaborn? [User Opinons Welcome]

  #83 opened a year ago by dbdimitrov
  5

• Difference on dotplot when running Steady-state Ligand-Receptor inference vignette from the Rank Aggregate section

  #81 opened a year ago by maximelepetit
  3