saezlab/decoupleR

Issues

• Error: C stack usage 7974412 is too close to the limit

  #149 opened 8 days ago by Clapton9527
  1

• get_progeny Error: no applicable method for 'rename' applied to an object of class "list"

  #143 opened 2 months ago by bbowles1
  4

• decoupleR::get_collectri [WARN]

  #147 opened 17 days ago by Xinlei672
  2

• Failed to download annotation resource `PROGENy` from OmniPath

  #148 opened 17 days ago by Urja25
  2

• "get_collectri" function cannot connect

  #146 opened 18 days ago by Yenlab-Q
  2

• GSEA_analysis

  #99 opened a year ago by mms100
  9

• Number of matched genes in pathway analysis

  #113 opened 10 months ago by kiwipeel
  3

• Question about pathway analysis

  #145 opened a month ago by kiwipeel
  0

• Could not find function get_collectri

  #138 opened 3 months ago by cf98
  5

• get_collectri broken from omnipathdb.org website being down

  #144 opened a month ago by omsai
  1

• get_progeny and organism = 'mouse' reports an error

  #129 opened 6 months ago by fedenichetti
  6

• Question about running pathways activity inference

  #142 opened 2 months ago by MigleMi
  1

• Incorporating a network model into an MLM

  #137 opened 3 months ago by rbutleriii
  1

• Subscript out of bounds error

  #130 opened 2 months ago by savagesr
  11

• decoupler script crashes because it uses all CPUs

  #136 opened 2 months ago by ahmedasadik
  1

• Error in `rlang::set_names()` get_progeny mouse

  #135 opened 2 months ago by bioshot-dotcom
  2

• differential expression analysis and GSEA

  #119 opened 2 months ago by Sophon-0
  8

• Computed TF activity is high but TF expression is low in scRNA-seq data

  #141 opened 2 months ago by kasayadior
  1

• Error in if (.keep) . else select(., -!!evs_col) from get_collectri(organism='human', split_complexes=FALSE)

  #140 opened 2 months ago by kasayadior
  2

• Error in get_collectri() from OmnipathR: Argument length zero and partial match warning

  #139 opened 3 months ago by ranxm2
  3

• Error in do.call(stop, list(m), envir = env)

  #132 opened 5 months ago by Megan0921
  2

• run_ulm taking very long to run and no feedback on progress

  #127 opened 6 months ago by gilstel
  3

• GSVA error

  #125 opened 6 months ago by victorcat4
  1

• get_progeny fails when using `organsim = "mouse"`

  #128 opened 7 months ago by Christian-Heyer
  10

• Can't get PROGENy model by get_progeny

  #126 opened 7 months ago by leeyangyangyang
  7

• TF analysis between conditions scRNA

  #118 opened 7 months ago by kiwipeel
  9

• High TF activity with few significant genes

  #116 opened 7 months ago by laurie-tonon
  3

• TF target genes in decoupleR analysis of scRNA-seq data

  #122 opened 8 months ago by JinSooJoo
  3

• Prepare for upcoming Seurat v5 release

  #94 opened 8 months ago by Gesmira
  0

• Error in get_collectri()

  #121 opened 9 months ago by FoMooo
  2

• scRNA TF activity inference

  #117 opened 10 months ago by SofyaMa
  2

• Pathway activity inference from scRNA-seq tutorial produces wrong results?

  #112 opened 10 months ago by kiwipeel
  1

• get_collectri is not able to fetch the right organism

  #115 opened 10 months ago by tamerbio
  6

• Transcription factor activity inference

  #114 opened 10 months ago by ramyavenk
  2

• Problems to understand the analysis of the tutorial

  #110 opened 10 months ago by Gregjlt
  3

• Question about TF activity inference analysis in single cell integrated datasets

  #111 opened 10 months ago by ChrisTzaferis
  2

• Use FindAllMarkers to detect top TFs per cluster in scRNA data

  #108 opened a year ago by akramdi
  1

• Error after get_resource() and check_repeated_edges(network)

  #107 opened a year ago by sciotlos
  2

• DESeq2 input for Transcription factor activity inference in bulk RNA-seq

  #104 opened a year ago by t1nnenissen
  1

• TF activities in single-cell: `run_ulm` takes too long

  #106 opened a year ago by nicholaslimwy
  2

• get_collectri is hard coded for human

  #109 opened a year ago by karJac
  2

• How to deal with gene readouts that are biased by gene length?

  #103 opened a year ago by jgoldmann
  2

• Are TPMs better than counts for the linear model?

  #100 opened a year ago by andreyurch
  1

• Pamgene S100 values to t-values

  #93 opened a year ago by DuruTuncer
  1

• Error: error in `str_to_upper()` OmnipathR

  #105 opened a year ago by maartenciers
  2

• get_collectri ignores organism parameter setting

  #102 opened a year ago by woblkilr
  4

• Interpretation of TF Activity

  #96 opened a year ago by lizzyjoan
  2

• Network is empty after intersecting it with mat

  #98 opened a year ago by JinSooJoo
  8

• Error in `map2()`

  #97 opened a year ago by noranekonobokkusu
  2

• get_collectri error

  #95 opened a year ago by t1nnenissen
  5