ctlab/fgsea

Issues

• plotCoregulationProfileSpatial for Seurat5 object with layers

  #163 opened 2 months ago by csmoreno
  4

• P value reproducibility

  #162 opened 2 months ago by jac-thom
  2

• Understandig GESECA results

  #161 opened 3 months ago by Teulip
  2

• Support for multiple samples in plotCoregulationSpatial

  #150 opened 3 months ago by assaron
  0

• fgsea hangs forever for highly enriched pathways in the presence of repeated high scored genes

  #151 opened 9 months ago by guidohooiveld
  9

• How to prepare pathway used for fgsea function

  #159 opened 5 months ago by yulchen810
  5

• Understanding the scoreType

  #155 opened 5 months ago by alkurowska
  2

• Error in preparePathwaysAndStats

  #149 opened 7 months ago by TX-Xiao
  5

• add rank plot for the GSEA plot

  #158 opened 6 months ago by person-c
  0

• fgseaMultilevelCpp doens't seem to be installed

  #138 opened 7 months ago by G3N0M3
  6

• Non-deterministic output with seed set, `nproc = 1`, and newest version

  #145 opened 7 months ago by chriswzou
  3

• GSEA to discover mixed enriched terms

  #154 opened 7 months ago by mauritsunkel
  5

• Implementation question

  #153 opened 8 months ago by mauritsunkel
  5

• Question: Geseca output, column "size"

  #152 opened 9 months ago by oswaldbra12
  4

• Spatial Code Error in base::colSums

  #126 opened 2 years ago by DirtyHarry80
  5

• are there p-value calculated for each leading edge gene?

  #148 opened a year ago by Leran10
  2

• fgsea giving identical padj values across many pathways

  #144 opened a year ago by johnse
  1

• Try to understand how ES is calculated

  #147 opened a year ago by ghbore
  3

• Question: scaling size of spots

  #146 opened a year ago by jyoo19
  2

• Gene filtering for FGSEA

  #143 opened a year ago by SirKuikka
  0

• Prepare for upcoming Seurat v5 release

  #142 opened a year ago by Gesmira
  0

• How to report for enriched gene sets?

  #140 opened a year ago by Close-your-eyes
  2

• minSize and maxSize

  #139 opened a year ago by ag1805x
  1

• Question: unbalanced gene-level statistic warning

  #124 opened a year ago by TatiKarp
  7

• Question: about scoreType = 'pos'

  #123 opened a year ago by noblegasss
  1

• Questions related to fgsea algorithm

  #120 opened a year ago by lucolotto
  1

• GESECA: Error following tutorial: 2 arguments passed to 'cumsum' which requires 1

  #136 opened a year ago by grapefruitshark
  5

• Citation

  #116 opened 2 years ago by pstew
  3

• Obtain per-sample expression value for a gene set

  #137 opened 2 years ago by PatrickMaclean
  1

• Question: Visium Data and pulling out cells with high GO enrichment for a given pathway

  #127 opened 2 years ago by DirtyHarry80
  8

• Insignificant p-values

  #135 opened 2 years ago by SirKuikka
  4

• Question: distribution requirements of statistics

  #134 opened 2 years ago by kvittingseerup
  3

• Does fGSEA require minSize as well?

  #130 opened 2 years ago by MEladawi
  1

• Will fgsea remove the wrong gene names in the input gene list?

  #132 opened 2 years ago by QichenFU
  1

• Error in calcGseaStatCumulativeBatch

  #133 opened 2 years ago by kevincjnixon
  4

• Stats should be named

  #129 opened 2 years ago by been9312
  1

• Which genes should I use?

  #131 opened 2 years ago by dekan-aleksandr
  2

• Question: Understanding discrepant results when using different ranking approaches and algorithmic parameters

  #128 opened 2 years ago by atakanekiz
  2

• GESECA function not existing

  #125 opened 2 years ago by DirtyHarry80
  3

• error: Value of SET_STRING_ELT() must be a 'CHARSXP' not a 'NULL' appearing when launching fgsea()

  #122 opened 2 years ago by klai001
  0

• Use outside of R

  #121 opened 2 years ago by maxkfranz
  4

• Subset of genes

  #119 opened 2 years ago by gjhuizing
  2

• is there a plan to implement fast ssGSEA?

  #117 opened 2 years ago by Yunuuuu
  3

• p.val threshold error in collapsePathways ()

  #115 opened 2 years ago by acaulier
  2

• A weird result: Highly enrichement visually but p value is not significant

  #114 opened 2 years ago by chent5
  6

• Problematic p-value histogram from fgsea (scoreType='pos')

  #111 opened 3 years ago by kvittingseerup
  3

• problem of fgseaMultilevel

  #112 opened 3 years ago by FionaMoon
  4

• Results are not reproducible

  #110 opened 3 years ago by korommatyi
  3

• Info on running multi-condition geseca

  #109 opened 3 years ago by kvittingseerup
  5

• enrichment score seems to have inverse sign

  #108 opened 3 years ago by EBosi
  2