HelenaLC/muscat

Issues

• aggregateData does not return colData

  #135 opened 15 days ago by Nayrouz109
  2

• I cannot compute pbHeatmap

  #133 opened 4 months ago by bkheira
  1

• pbDS(pb, design = mm, contrast = contrast) error

  #136 opened a month ago by Jadeapple
  2

• Multiple Random Effects

  #134 opened 2 months ago by jgockley62
  4

• Loss of clusters during pbDS

  #132 opened 4 months ago by bkheira
  3

• How do I use muscat if my single cell data comes from different datasets with clear batch effects?

  #130 opened 6 months ago by WyzhaoJo
  2

• Doubt in sim_mean and ground truth

  #131 opened 6 months ago by cakeinspace
  1

• limma-voom implementation results in more false positives than expected

  #129 opened 8 months ago by reubenthomas
  4

• pbDS limma-voom method appears to ignore voom weights after computing them

  #119 opened a year ago by DarwinAwardWinner
  2

• Error installing muscat

  #128 opened 8 months ago by MJGGaray
  1

• How is the AveExpr in mmDS calculated?

  #127 opened 9 months ago by Lila3141
  0

• limma voom cpm values

  #126 opened 9 months ago by AnjaliC4
  0

• possible bug in resDS for some methods

  #102 opened 2 years ago by AnjaliC4
  0

• DP simulated data has inverted logFC and only one bimodal group

  #125 opened a year ago by ChristophH
  3

• Doubt in terminology

  #123 opened a year ago by cakeinspace
  2

• error with pbDS: how to set the correct parameters

  #108 opened a year ago by yamihn
  1

• aggregateData returns all zero when there is only 1 sample_id

  #124 opened a year ago by jsialar
  1

• How to correct batch effects when using muscat?

  #122 opened a year ago by ChenyuZhang97
  2

• muscat_analysis don't accept DICE annotation

  #120 opened a year ago by obotman
  15

• Specifying contrasts in MUSCAT mixed models

  #118 opened a year ago by ismailelshimy
  6

• pbHeatmap y %in% assayNames(x) is not TRUE

  #121 opened a year ago by amoyguang1
  8

• How to do sth like contrast for cell level DE analysis

  #117 opened a year ago by pariaaliour
  2

• res <- pbDS(pb, verbose = FALSE) Error in x[[1]] : subscript out of bounds

  #116 opened 2 years ago by Jungkooklove0901
  3

• Error using aggregateData with example_sce

  #115 opened 2 years ago by yannk-lm
  4

• A constraint that might not be required in PrepSim

  #113 opened 2 years ago by onahman
  2

• MUSCAT Mixed Effects Models and the Cellular Detection Rate

  #114 opened 2 years ago by ismailelshimy
  2

• mm_glmm("nbinom") returns NAs

  #111 opened 2 years ago by Nayrouz109
  0

• mmDS() and logcounts

  #110 opened 2 years ago by Nayrouz109
  4

• Mixed model approach with paired sample design

  #109 opened 2 years ago by hayfre
  2

• pbHeatmap error because 't' is not implemented for 'Matrix'

  #93 opened 2 years ago by AnaBVA
  3

• quick question about filtering of genes

  #100 opened 2 years ago by AnjaliC4
  1

• Error in .check_args_pbHeatmap

  #105 opened 2 years ago by lindsaynhayes
  5

• Analysing DEG in Spatial visium data

  #103 opened 2 years ago by vkjain0006
  2

• Possible bug in simData function

  #104 opened 2 years ago by simonemodolo
  0

• Adding pseudobulk-level covariates defined across cell types, to a DE/DS analysis

  #101 opened 2 years ago by koenvandenberge
  1

• Error: BiocParallel errors element index: 4, 5 first error: missing value where TRUE/FALSE needed

  #95 opened 2 years ago by kmh005
  3

• Error: BiocParallel errors element index: 5, 6, 7, 8, 9, 10, ... first error: logical subscript contains NA

  #89 opened 2 years ago by charlesgwellem
  2

• muscat with no replicates?

  #90 opened 2 years ago by nuriabonetm
  1

• How to set up interactions?

  #99 opened 2 years ago by AnjaliC4
  1

• cannot compute log geometric means Deseq2

  #97 opened 2 years ago by AnjaliC4
  2

• error in vst sctransform

  #98 opened 2 years ago by ktyssowski
  2

• p_adj.loc greater than p_adj.glb

  #96 opened 2 years ago by malosreet
  2

• Importing seurat object directly to muscat

  #88 opened 2 years ago by ps120195
  5

• full list of genes

  #94 opened 2 years ago by AnaBVA
  1

• Muscat compared to Distinct

  #92 opened 2 years ago by chris-rands
  1

• Example code from prepSCE does not work with aggregateData

  #91 opened 2 years ago by dariober
  1

• Error when simulating data use my own sce object

  #84 opened 2 years ago by wanghao98
  10

• Potential bug in the prepSim code

  #86 opened 2 years ago by wanghao98
  1

• pbHeatmap doesn't match DS gene list?

  #85 opened 2 years ago by SimoniMD
  2

• weighting the samples according to the number of cells

  #87 opened 3 years ago by stkachev
  0