campbio/celda

Issues

• crash: "The number of rows in 'eta' must be equal to the number of rows in 'counts'." when specifying a background argument

  #361 opened 3 years ago by plijnzaad
  9

• Installing on M1 Macbook fails

  #395 opened 9 months ago by kotr98
  7

• Error: package or namespace load failed for ‘celda’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘GenomeInfoDbData’

  #400 opened 9 months ago by zijunmeng
  1

• Is it necessary to filter gene or cell filter needed after DecontX

  #391 opened a year ago by MISAKA-DaYu
  1

• Disagreement in contamination estimations with/without raw data

  #390 opened a year ago by dlee598
  1

• High level of estimated contamination for same sample but different set of filtered cells

  #384 opened 2 years ago by dlee598
  1

• Decontx: Heuristic clustering or z parameter? How are the cluster labels specified with the z parameter affecting the decontamination?

  #376 opened 2 years ago by MartaSanchezCarbonell
  1

• decontX not reproducible?

  #377 opened 2 years ago by trnguyenuka
  3

• decontX failure in all matrix types

  #369 opened 2 years ago by CMSimpson8
  2

• using decontx with filtered or raw matrix?

  #374 opened 2 years ago by dm8000
  1

• Getting percentages of contamination

  #371 opened 2 years ago by sameehan2301
  1

• different genes

  #370 opened 2 years ago by wbf520qcp
  1

• plotDecontXMarkerPercentage omit celltype when it has two clusters concatenated

  #323 opened 2 years ago by makloufg
  7

• Using DecontX

  #367 opened 2 years ago by barbarashih
  1

• Error in fitTrendVar(fm, fv, ...)

  #351 opened 2 years ago by ayeTown
  3

• Unexpected behavior when subsetting on decontaminated counts

  #364 opened 2 years ago by jmodlis
  1

• cells with 100% contamination?

  #362 opened 2 years ago by plijnzaad
  3

• decontX output not found

  #360 opened 3 years ago by hsriniva1104
  1

• Algorithm stuck at last iteration in Estimating contamination

  #352 opened 3 years ago by ayeTown
  3

• background argument is ignored

  #355 opened 3 years ago by jdekanter
  5

• Threshold to filter contaminated cells

  #353 opened 3 years ago by supermegamio
  2

• Error in ‘reducedDim’ for UMAP

  #349 opened 3 years ago by karlaarz
  1

• "Unused argument background" error

  #346 opened 3 years ago by sjfleming
  3

• use of decontXcounts in subseq

  #344 opened 3 years ago by Sa753
  1

• using decontX on combined object, or on each sample individually?

  #334 opened 3 years ago by gruensch
  1

• Error while using 'recursiveSplitModule'

  #331 opened 3 years ago by linxy29
  3

• Sequencing depth corrected counts

  #319 opened 4 years ago by faraz89
  5

• Deprecate the use of plotHeatmap

  #325 opened 4 years ago by zhewa
  0

• Problem Running decontX with z argument

  #320 opened 4 years ago by astarr97
  19

• Plot perplexity labels

  #322 opened 4 years ago by joshua-d-campbell
  1

• Round or integer?

  #318 opened 4 years ago by faraz89
  1

• error while using decontX on seurat data (count object)

  #316 opened 4 years ago by mbourgey
  5

• plotDimReduceCluster error

  #308 opened 4 years ago by ltosti
  2

• colnames/rownames of counts

  #233 opened 4 years ago by joshua-d-campbell
  1

• Should there be seed setting for recursiveSplitModule / recursiveSplitCell ??

  #263 opened 4 years ago by Irisapo
  2

• building the vignettes during installation fails

  #297 opened 4 years ago by vertesy
  3

• NAs produced by integer overflow

  #287 opened 4 years ago by ncasiraghi
  3

• DecontX vignette - clarify that input matrix is from pre-filtered barcodes

  #292 opened 4 years ago by rdalbanus
  0

• DecontX unused argument error

  #296 opened 4 years ago by supfastjf
  2

• Error in if (min(x) == 0) { : missing value where TRUE/FALSE needed

  #295 opened 4 years ago by peerkarmaus
  4

• DecontX before or after integrating datasets?

  #273 opened 4 years ago by hummuscience
  6

• Cannot run decontX on SCE dataset.

  #268 opened 4 years ago by piyushjo15
  4

• seed should always be set as default in terms of reproducibility

  #237 opened 4 years ago by Irisapo
  2

• remove 0 transcript genes for decontx

  #262 opened 4 years ago by Irisapo
  1

• Does decontX() gives out a correct count matrix?

  #269 opened 4 years ago by piyushjo15
  2

• DecontX adding counts?

  #254 opened 5 years ago by juliaszusz
  1

• dependency on BiocNeighbors?

  #261 opened 5 years ago by Irisapo
  2

• celda package version need to be corrected

  #232 opened 5 years ago by Irisapo
  0

• Need to bump BiocManager version

  #225 opened 5 years ago by Irisapo
  0

• customizable cluster labels in plotDimReduceCluster()

  #226 opened 5 years ago by timofoloyo
  0