rcastelo/GSVA

Issues

• Enforce non-empty assay names for SummarizedExperiment and subclasses

  #229 opened 17 days ago by axelklenk
  0

• Error with ssgseaParam

  #226 opened 25 days ago by kaqisekuzi
  1

• Filter genes with constant expression in spatCor()

  #225 opened a month ago by rcastelo
  0

• error matrixStats

  #222 opened a month ago by jmzhang1911
  1

• Parallelization of spatCor()

  #224 opened a month ago by rcastelo
  0

• How to rewrite? Is there a change in the way GSVA operates?

  #188 opened 7 months ago by lucienhan94
  2

• Scaling of ssgsea results depending upon gene list size

  #221 opened 2 months ago by dfermin
  1

• Applying ssGSEA on Spatial Transcriptomics Visium data

  #223 opened 2 months ago by han9978
  1

• Error when using Data Input From Workspace in Shiny app

  #209 opened 5 months ago by axelklenk
  3

• Negative length vectors are not allowed for large dataset

  #217 opened 2 months ago by Zhixuan-Jing
  1

• Error in h(simpleError(msg, call))

  #219 opened 2 months ago by sunta3iouxos
  3

• Error with Plage method on Windows

  #220 opened 2 months ago by jordimartorell
  1

• Why no longer run the function as before using the original code?

  #218 opened 4 months ago by wuxiangning
  0

• Most Data Being Filtered

  #204 opened 5 months ago by abadgerw
  5

• ssGSEA Conceptual Questions

  #205 opened 5 months ago by abadgerw
  12

• Support for GSEA plots

  #192 opened 5 months ago by cihanerkut
  8

• Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct

  #213 opened 5 months ago by lucyu2668
  1

• Extend the GSVA shiny app to make use of its new missing data policy

  #215 opened 5 months ago by axelklenk
  0

• Implement a missing data policy for GSVA

  #211 opened 5 months ago by rcastelo
  0

• Store internal GSVA ranks to enable enrichment plots and flexible scoring

  #200 opened 5 months ago by rcastelo
  0

• Missing Data

  #203 opened 5 months ago by abadgerw
  1

• Improve annotation mapping through readGMT()

  #177 opened 6 months ago by rcastelo
  0

• kcdf: in ssgseaParam，do we still need to set kcdf?

  #201 opened 6 months ago by Stefanhxw
  1

• Some

  #199 opened 7 months ago by junglingfish
  0

• Improve messages to the user

  #197 opened 7 months ago by rcastelo
  0

• GSVA.so: undefined symbol: match5

  #184 opened 7 months ago by bbimber
  5

• matrixStats error

  #196 opened 7 months ago by andreyurch
  1

• Add a new default 'auto' argument to the 'kcdf' parameter in the GSVA method

  #193 opened 7 months ago by rcastelo
  0

• Create a FAQ

  #191 opened 7 months ago by rcastelo
  0

• Perform ECDF estimation with Gaussian kernels on sparse matrices

  #189 opened 7 months ago by rcastelo
  0

• Can ssGSEA be performed when the number of genes in the reference gene set is very small?

  #186 opened 7 months ago by Chamberlain1993
  4

• How should ssGSEA be performed on GEP data?

  #187 opened 8 months ago by csu-lzj
  2

• How to Set the 'zscore' Method in Recent Versions of GSVA Analysis?

  #185 opened 8 months ago by Li-mengjie
  2

• Problems encountered when calculating GSVA with large single-cell data

  #178 opened 8 months ago by sjasws
  7

• Calculate Moran's I on the rows of a spatialExperiment object

  #179 opened 8 months ago by rcastelo
  0

• Result of gsva is all NA

  #168 opened 8 months ago by YihengJiang0912
  13

• Calling gsva is defunct, use a method-specific parameter object (error)

  #172 opened 9 months ago by LnOp16
  1

• Implement a missing data policy for ssGSEA

  #174 opened 9 months ago by rcastelo
  0

• Association between pathway score of two pathways

  #176 opened 9 months ago by Chrisdoan9
  2

• Fail to compiling on HDF5

  #165 opened 10 months ago by yifanfu01
  1

• Error: Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct; use a method-specific parameter object (see '?gsva').

  #173 opened 10 months ago by jiangych17
  1

• The data type of exprData matrix: for ssgseaParam, integer counts? Continuous expression data?

  #171 opened 10 months ago by jnhv
  2

• gsva()function

  #170 opened 10 months ago by eliauk07yz
  2

• res <- igsva() seem not work when use data from workspace

  #166 opened a year ago by DDL095
  2

• Load GMT files dealing duplicated gene sets

  #158 opened a year ago by rcastelo
  0

• WARNING Missing link or links in documentation object 'gsva.Rd': ‘dgCMatrix’

  #160 opened a year ago by axelklenk
  0

• Provide filtered gene sets sizes

  #157 opened a year ago by rcastelo
  0

• Type of output from gsva()

  #155 opened a year ago by Chrisdoan9
  7

• reconsider S4 class hierarchy

  #156 opened a year ago by axelklenk
  0

• Number of pathway output

  #154 opened a year ago by Chrisdoan9
  5