kharchenkolab/cacoa

Issues

• What exactly is being plotted with plotCellLoadings?

  #54 opened 4 months ago by milddaa
  2

• Error calling `estimateExpressionShiftMagnitudes` function with Seurat object

  #49 opened a year ago by mkazanov
  3

• What does a negative expression distance mean?

  #55 opened 4 months ago by ThomasLLi
  0

• estimateMetadataSeparation gives error

  #51 opened a year ago by Laura19993
  6

• plotSampleDistances with metadata gives error

  #52 opened 4 months ago by Laura19993
  5

• invalid character indexing when running estimateClusterFreeDE

  #46 opened a year ago by amissarova
  2

• `estimateMetadataSeparation` with `space = "pseudo.bulk"` returns error

  #50 opened a year ago by rrydbirk
  0

• estimateClusterFreeExpressionShifts() produces all NaN

  #37 opened a year ago by rrydbirk
  3

• Cacoa not working with Seurat object

  #48 opened a year ago by adityamahadevaniyer
  2

• plotOntologyHeatmapCollapsed function got an error

  #45 opened 2 years ago by Angel-Wei
  9

• estimateMetadataSeparation() gave an error - "object 'n.permutations' not found"

  #47 opened 2 years ago by Angel-Wei
  5

• Move checkPackageInstalled to sccore

  #34 opened 2 years ago by rrydbirk
  1

• unable to use Cacoa on a seurat object

  #39 opened 2 years ago by GhobrialMoheb
  7

• Troubles with estimateExpressionShiftMagnitudes() and estimateDiffCellDensity() functions

  #21 opened 3 years ago by anastasiiaNG
  10

• fails when sample.groups describes a subset of samples

  #28 opened 3 years ago by pkharchenko
  0

• ClusterFreeExpression Not S4 object

  #29 opened 3 years ago by jayp2919
  3

• Installation errors

  #41 opened 2 years ago by daniel-spies
  1

• estimateCellLoadings fails when less than 3 cell types

  #43 opened 2 years ago by rrydbirk
  1

• Warning in plotClusterFreeExpressionShifts()

  #36 opened 2 years ago by rrydbirk
  1

• Warning in estimateClusterFreeExpressionShifts()

  #35 opened 2 years ago by rrydbirk
  1

• cao$plotOntology() filtering by "up" and "down"dos not work

  #32 opened 2 years ago by Laura19993
  2

• estimateCellLoadings() fails: object 'mx.first' not found

  #38 opened 2 years ago by rrydbirk
  1

• Error: dimension should be positive

  #33 opened 3 years ago by cubense
  2

• Encounted an Error in if (maxP > -minP) { : missing value where TRUE/FALSE needed

  #31 opened 3 years ago by ZeroKeng
  4

• Understanding resampling parameters for DEG analysis

  #24 opened 3 years ago by Laura19993
  5

• estimateClusterFreeDE returns only NaNs and 0s (seurat object)

  #30 opened 3 years ago by amissarova
  3

• Add a vignette explaining parameters for all analyses

  #27 opened 3 years ago by VPetukhov
  0

• palette argument in plotSampleDistances works only for discrete covariates

  #18 opened 3 years ago by VPetukhov
  1

• Passing `data.object=NULL` makes passing `embedding` mandatory

  #25 opened 3 years ago by VPetukhov
  1

• Add some ways to invalidate cache

  #3 opened 3 years ago by VPetukhov
  1

• sample.groups are not extracted automatically anymore

  #13 opened 3 years ago by rrydbirk
  1

• Troubles with estimateExpressionShiftMagnitudes()

  #22 opened 3 years ago by JarningGau
  2

• estimateDiffCellDensity() drops negative values

  #26 opened 3 years ago by rrydbirk
  3

• Roxygen2 documentation

  #15 opened 3 years ago by evanbiederstedt
  0

• Possible wrong contour for overlapping

  #19 opened 3 years ago by hiraksarkar
  4

• no dependency on psych package declared

  #16 opened 4 years ago by pkharchenko
  4

• estimateExpressionShiftMagnitudes uses all available cores

  #10 opened 4 years ago by rrydbirk
  1

• object 'cda' not found in getCdaLoadings

  #11 opened 4 years ago by VPetukhov
  2

• Improve localZScores calculation

  #9 opened 5 years ago by rrydbirk
  3

• Notch error in plotExpressionShiftMagnitudes

  #4 opened 5 years ago by rrydbirk
  1

• Incorporate DE estimations

  #7 opened 5 years ago by rrydbirk
  2

• Unused argument

  #8 opened 5 years ago by rrydbirk
  6

• estimateExpressionShiftMagnitudes uses all available memory

  #6 opened 5 years ago by rrydbirk
  3

• Store "groups" in the Cacoa object

  #2 opened 5 years ago by VPetukhov
  7

• "Cacoa" is not exported to environment

  #1 opened 5 years ago by rrydbirk
  1