saezlab/decoupler-py

Issues

• Marsilea error in dc.plot_associations()

  #144 opened 4 months ago by dnjst
  1

• Error when running get_pseudobulk(): AttributeError: 'csr_matrix' object has no attribute 'A'

  #141 opened 4 months ago by raquelgarza
  3

• Warnings about annotations raised when running `dc.plot_targets`

  #140 opened 4 months ago by Fantasque68
  1

• Dataloading

  #142 opened 4 months ago by Intron7
  1

• dc.get_pseudobulk needs to use '.todense()' instead of '.A'

  #146 opened 4 months ago by jhaberbe
  2

• psbulk_counts are associated with top PCs

  #138 opened 4 months ago by singlecellfan
  5

• module 'decoupler' has no attribute 'plot_network'

  #137 opened 4 months ago by linanzhang
  1

• GSEA handling missing genes

  #132 opened 5 months ago by tboen1
  5

• AttributeError: 'csr_matrix' object has no attribute 'A'

  #139 opened 5 months ago by MarwaneBourdim
  6

• Inferring TF activity using custom GRN

  #133 opened 5 months ago by AmelZulji
  4

• numba version 0.60.0

  #135 opened 5 months ago by Intron7
  6

• Issue with omnipath and dc.translate_net(msigdb, target_organism = 'mouse', unique_by = ('geneset', 'genesymbol'))

  #131 opened 5 months ago by dantyrr
  3

• matplotlib.cm.get_cmap is removed from version 3.9

  #127 opened 5 months ago by zhaleh-safikhani
  2

• Detection of type of alteration in each signaling pathway in each cell type

  #130 opened 5 months ago by ngvananh2508
  6

• Progeny mouse 'Invalid block type' error

  #128 opened 5 months ago by eaboelno
  4

• ORA analysis get hung in jupyter notebook

  #126 opened 5 months ago by zhaleh-safikhani
  1

• plot_network doesnt return a graph with right node/edge visual styles

  #125 opened 6 months ago by zhaleh-safikhani
  1

• Progeny pvals

  #122 opened 6 months ago by nicolebussola
  1

• keyerror when running dc.get_ora_df

  #129 opened 6 months ago by wangjiawen2013
  1

• why ulm (and not mlm) for transription factor activities ? there must be some overlaps

  #120 opened 6 months ago by Sophon-0
  1

• plot_network function top target

  #119 opened 6 months ago by Sophon-0
  1

• Getting pval=0 for various enriched pathways after running GSEA

  #124 opened 6 months ago by saksham132
  2

• Problem when using dc.get_contrast()

  #123 opened 6 months ago by derekchen7
  2

• Is run_aucell thread-safe to run in a multi-threaded script?

  #118 opened 7 months ago by pcm32
  3

• run_ulm on TF with only positively regulated target genes

  #117 opened 7 months ago by ken-chen-18
  2

• Error while translating human to mouse MSigDB

  #109 opened 7 months ago by wbrett87
  6

• Failed to download `CollecTRI` from OmniPath. Invalid value `loops` for `InteractionsQuery`. AttributeError: module 'omnipath' has no attribute 'static'

  #108 opened 7 months ago by clg12
  1

• PLOT issues

  #114 opened 8 months ago by Sophon-0
  2

• dc.run_mlm only returning data for 1 source

  #115 opened 8 months ago by aalockhart1
  2

• Loading resources for mouse is not working

  #102 opened 8 months ago by riederd
  9

• EOFError: Compressed file ended before the end-of-stream marker was reached

  #105 opened 8 months ago by ChangLu92
  2

• Verbose output from bencharking pipeline seems to say 'for 25 unique sources' despite more sources

  #111 opened 8 months ago by IBMB-MFP
  2

• Cannot convert gene symbol to rat

  #110 opened 8 months ago by wangjiawen2013
  5

• Nan values in benchmarking pipeline still give error - Decoupler v 1.6

  #106 opened 9 months ago by IBMB-MFP
  2

• decoupler.plot_barplot ax

  #104 opened 9 months ago by annita-louloupi
  3

• copy.deepcopy() in get_contrast()

  #107 opened 9 months ago by wan-nie
  2

• Flag for sorting of gene names

  #103 opened 9 months ago by leoTiez
  4

• run_ora_df

  #101 opened 10 months ago by mcjmigdal
  2

• Limiting usage of cores or threads

  #99 opened a year ago by racng
  2

• Functional PB Tutorial fails at dc.plot_associations

  #94 opened a year ago by jan-engelmann
  5

• Get gene markers used to annotate the cell type

  #91 opened a year ago by ryrl9703
  2

• Announcement: some Galaxy modules for some decoupler functionalities

  #97 opened a year ago by pcm32
  1

• Method dc.run_gsva error

  #90 opened a year ago by chuiqin
  2

• method run_gsea() error : SystemError: CPUDispatcher(<function nb_gsea at 0x7f7477d3b9c0>) returned a result with an exception set

  #88 opened a year ago by nicolas-zimmermann
  6

• dc.get_collectri() does not work

  #95 opened a year ago by FADHLyemen
  2

• dc.get_progeny(organism = 'mouse') fails with ImportError

  #92 opened a year ago by riederd
  5

• ValueError: Invalid value `loops` for `InteractionsQuery` in dc.get_collectri()

  #93 opened a year ago by GERMAN00VP
  2

• shuffle_net output not random

  #87 opened a year ago by IBMB-MFP
  1

• Error downlaoding progeny model for mouse species

  #86 opened a year ago by archanabhardwaj
  3

• Pseudobulk for each sample

  #89 opened a year ago by SNOL2
  2