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HelenaLC
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muscat
Multi-sample multi-group scRNA-seq analysis tools
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latent variables
#138
Flu09
opened
1 month ago
0
Problems with RNA ambient
#137
hahmu
closed
2 months ago
2
pbDS(pb, design = mm, contrast = contrast) error
#136
Jadeapple
opened
3 months ago
2
aggregateData does not return colData
#135
Nayrouz109
closed
3 months ago
2
Multiple Random Effects
#134
jgockley62
opened
4 months ago
4
I cannot compute pbHeatmap
#133
bkheira
opened
6 months ago
2
Loss of clusters during pbDS
#132
bkheira
closed
6 months ago
3
Doubt in sim_mean and ground truth
#131
cakeinspace
opened
9 months ago
1
How do I use muscat if my single cell data comes from different datasets with clear batch effects?
#130
WyzhaoJo
closed
8 months ago
2
limma-voom implementation results in more false positives than expected
#129
reubenthomas
opened
10 months ago
4
Error installing muscat
#128
MJGGaray
closed
10 months ago
1
How is the AveExpr in mmDS calculated?
#127
Lila3141
opened
1 year ago
0
limma voom cpm values
#126
AnjaliC4
opened
1 year ago
0
DP simulated data has inverted logFC and only one bimodal group
#125
ChristophH
opened
1 year ago
3
aggregateData returns all zero when there is only 1 sample_id
#124
jsialar
closed
1 year ago
1
Doubt in terminology
#123
cakeinspace
closed
1 year ago
2
How to correct batch effects when using muscat?
#122
ChenyuZhang97
closed
1 year ago
2
pbHeatmap y %in% assayNames(x) is not TRUE
#121
amoyguang1
closed
1 year ago
8
muscat_analysis don't accept DICE annotation
#120
obotman
closed
1 year ago
15
pbDS limma-voom method appears to ignore voom weights after computing them
#119
DarwinAwardWinner
opened
1 year ago
2
Specifying contrasts in MUSCAT mixed models
#118
ismailelshimy
opened
1 year ago
6
How to do sth like contrast for cell level DE analysis
#117
pariaaliour
opened
1 year ago
2
res <- pbDS(pb, verbose = FALSE) Error in x[[1]] : subscript out of bounds
#116
Jungkooklove0901
closed
1 year ago
3
Error using aggregateData with example_sce
#115
yannk-lm
closed
1 year ago
4
MUSCAT Mixed Effects Models and the Cellular Detection Rate
#114
ismailelshimy
opened
1 year ago
2
A constraint that might not be required in PrepSim
#113
onahman
opened
1 year ago
2
norm in limma trend
#112
XikunHan
closed
1 year ago
0
mm_glmm("nbinom") returns NAs
#111
Nayrouz109
opened
1 year ago
0
mmDS() and logcounts
#110
Nayrouz109
closed
1 year ago
4
Mixed model approach with paired sample design
#109
hayfre
closed
2 years ago
2
error with pbDS: how to set the correct parameters
#108
yamihn
closed
1 year ago
1
Passing filter parameters to pbDS
#107
dbdimitrov
opened
2 years ago
1
Updated citation to journal publication
#106
molecules
closed
2 years ago
1
Error in .check_args_pbHeatmap
#105
lindsaynhayes
closed
2 years ago
5
Possible bug in simData function
#104
simonemodolo
opened
2 years ago
0
Analysing DEG in Spatial visium data
#103
vkjain0006
opened
2 years ago
2
possible bug in resDS for some methods
#102
AnjaliC4
opened
2 years ago
0
Adding pseudobulk-level covariates defined across cell types, to a DE/DS analysis
#101
koenvandenberge
opened
2 years ago
1
quick question about filtering of genes
#100
AnjaliC4
closed
2 years ago
1
How to set up interactions?
#99
AnjaliC4
closed
2 years ago
1
error in vst sctransform
#98
ktyssowski
closed
2 years ago
2
cannot compute log geometric means Deseq2
#97
AnjaliC4
opened
2 years ago
2
p_adj.loc greater than p_adj.glb
#96
malosreet
closed
2 years ago
2
Error: BiocParallel errors element index: 4, 5 first error: missing value where TRUE/FALSE needed
#95
kmh005
closed
2 years ago
3
full list of genes
#94
AnaBVA
closed
2 years ago
1
pbHeatmap error because 't' is not implemented for 'Matrix'
#93
AnaBVA
opened
2 years ago
3
Muscat compared to Distinct
#92
chris-rands
closed
2 years ago
1
Example code from prepSCE does not work with aggregateData
#91
dariober
closed
2 years ago
1
muscat with no replicates?
#90
nuriabonetm
closed
2 years ago
1
Error: BiocParallel errors element index: 5, 6, 7, 8, 9, 10, ... first error: logical subscript contains NA
#89
charlesgwellem
closed
2 years ago
2
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