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satijalab
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sctransform
R package for modeling single cell UMI expression data using regularized negative binomial regression
GNU General Public License v3.0
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arguments imply differing number of rows
#91
Biomiha
closed
3 years ago
6
Question about using residuals for integration & DE analysis
#90
jgamache014
closed
3 years ago
2
fixed batch variable or latent variable attribute checking
#89
kmwinkley
closed
3 years ago
1
SCTransform error when using batch or other latent variables
#88
kmwinkley
closed
3 years ago
1
sctransform: Error: node stack overflow
#87
duocang
closed
3 years ago
5
Error in make_cell_attr(umi, cell_attr, latent_var, batch_var, latent_var_nonreg, : cell attributes cannot contain any NA, NaN, or infinite values
#86
connorhknight
opened
3 years ago
11
SCTransform gives 'BLAS/LAPACK routine 'DLASCLS'" error
#85
spadavec
opened
3 years ago
5
lazy-load database '/home/yanxing/R/x86_64-pc-linux-gnu-library/4.0/sctransform/R/sctransform.rdb' is corrupt
#84
chenyx47
closed
3 years ago
1
Does sctransform normalisation account for changes in RNA composition?
#83
lucygarner
opened
3 years ago
1
reached iteration limit
#82
Pinpin-u1111
closed
3 years ago
4
Error in h(simpleError(msg, call)) when I was running SCTransform
#81
HuaZou
closed
3 years ago
1
SCTransform normalised data or regular log normalised data for assessing gene-gene correlations with pySCENIC?
#80
lucygarner
opened
3 years ago
0
About pbmc33k_identities.rds in paper
#79
kuang-da
opened
3 years ago
0
Construction of model and regularization when batch_var is used
#78
HillJamie
opened
3 years ago
0
How to specify genes for normalization?
#77
huoqiang138
opened
3 years ago
3
Error in while ((it <- it + 1) < limit && abs(del) > eps) { : missing value where TRUE/FALSE needed
#76
nasjr08
closed
3 years ago
8
intermittent errors in SCTransform
#75
kmwinkley
closed
3 years ago
2
No residual_variance with GlmGamPoi when using batch_var
#74
ATpoint
closed
3 years ago
4
error from signalConditions
#73
jliu678
closed
3 years ago
3
Issue when trying to upload shiny app
#72
MarcElosua
closed
3 years ago
2
"missing value where TRUE/FALSE needed" error occurring with certain seeds (for nb_fast and poisson both with theta.ml)
#71
diegoalexespi
closed
3 years ago
5
Difference between vst_out$y and get_residuals()
#70
frederikziebell
closed
3 years ago
2
Error in get_residuals(), 'log_umi' not found
#69
frederikziebell
opened
3 years ago
1
Consistency across computers/environments
#68
Baboon61
opened
3 years ago
3
FYI: sctransform 0.3.0 break package tests of Seurat
#67
HenrikBengtsson
closed
3 years ago
5
add glmGamPoi to increase SCT speed
#66
yuhanH
closed
3 years ago
11
Error in while ((it <- it + 1) < limit && abs(del) > eps) { : missing value where TRUE/FALSE needed
#65
morganee261
closed
3 years ago
10
Conceptual check-in: Avg Pearson residual as gene set score?
#64
dpcook
closed
3 years ago
2
Disk-based data
#63
willtownes
opened
3 years ago
4
Error in if (sum(outliers) > 0) { : missing value where TRUE/FALSE needed
#62
bluejek128
opened
3 years ago
3
sctransform error: Vector Memory Exceeded and/or methods to integrate replicates w/o using sctransform
#61
agurgis
closed
3 years ago
1
Feat/select gene
#60
yuhanH
closed
4 years ago
1
sctransform::vst could run faster
#59
dariomel
closed
3 years ago
3
apparently wrong logic in function vst
#58
dariomel
closed
3 years ago
2
SCTransform taking hours with very large memory demand
#57
liqianma7
opened
4 years ago
1
Memory friendly option for those interested only in corrected counts and HVGs
#56
gokceneraslan
closed
4 years ago
3
SCTransform on multiple batches
#55
Nusob888
opened
4 years ago
2
Mean and variance of normalized gene expression
#54
jmbreda
opened
4 years ago
1
Problems estimating theta
#53
iwillham
closed
4 years ago
2
`poisson` is used when `nb`?
#52
pengyu
closed
4 years ago
1
SCTransform Normalize Sequencing Depth
#51
ShaowenJ
opened
4 years ago
1
run.test vs. compare_expression
#50
alexander-7
closed
4 years ago
2
Compare expression vs. FindMarkers
#49
dagarfield
opened
4 years ago
0
Num of genes after VST
#48
haoyangz
closed
4 years ago
1
DE on SCTransformed and Integrated data
#47
rleonriv
closed
4 years ago
3
iteration limit reached - help
#46
ltosti
closed
4 years ago
1
NMF on residuals
#45
cnk113
closed
4 years ago
4
Error: Feature names of counts matrix cannot be empty
#44
mariafiruleva
closed
4 years ago
2
Comparison to linear regression
#43
pavlin-policar
opened
4 years ago
2
Spatial transcriptomics
#42
alextamburino
opened
4 years ago
1
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