issues
search
satijalab
/
sctransform
R package for modeling single cell UMI expression data using regularized negative binomial regression
GNU General Public License v3.0
203
stars
33
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Doubt Integratedata using normalization SCTransform
#138
PilanEli
closed
1 year ago
3
Difference between sctransform::vst() and SCTransform()?
#137
micw42
closed
2 years ago
5
Question about Reproducing a Plot in the Paper Introducing the SCTransform (Hafemeister, C., & Satija, R. #1999)
#136
mcap91
opened
2 years ago
2
Cannot install on arm64
#135
skilpinen
closed
2 years ago
2
warning: solve(): system is singular; attempting approx solution Error in h(simpleError(msg, call)) :
#134
lima1
closed
2 years ago
2
sctransform install; cannot find -lgfortran
#133
PiaoyangGuohai1
closed
2 years ago
1
do.scale = FALSE leads to many subpopulations in UMAP
#132
george-hall-ucl
closed
1 year ago
4
Error in make_cell_attr(umi, cell_attr, latent_var, batch_var, latent_var_nonreg, : cell attribute row names must match column names of count matrix
#131
AlonsoOga
closed
1 year ago
9
Error in h(simpleError(msg, call))
#130
jiayiliujiayi
closed
2 years ago
2
prepSCTFindMarkers data correction increased the fraction of zero values.
#129
yamajackr
closed
2 years ago
2
scale_factor
#128
z5ouyang
closed
2 years ago
2
Default clipping value: sqrt(n_cells/30) or sqrt(n_cells)?
#127
dkobak
closed
2 years ago
1
batch_var doesn't work with vst.flavor = 'v2'
#126
cnk113
opened
2 years ago
2
batch_var is not corrected in sctransform::correct
#125
dg520
opened
2 years ago
0
variable.features.n didn't change the number of genes used
#124
Evenlyeven
closed
2 years ago
1
Develop patch 1
#123
rsatija
closed
2 years ago
0
Question: Is it possible to reverse the scaling done by vst()?
#122
TeodoraTockovska
opened
2 years ago
4
Function future_lapply is using the default value 'future.seed = FALSE'
#121
adRn-s
closed
2 years ago
3
Reproducible SCTransform crash
#120
ms3389
closed
2 years ago
5
'node stack overflow' when using 'IntegrateData'!
#119
amssljc
opened
2 years ago
1
Selection of the number of cells used for the NB regression in SCTransform
#118
BiotechPedro
opened
2 years ago
0
Error when running SCtransform
#117
KaWingLee9
opened
2 years ago
1
Missing expm1?
#116
knokknok
closed
2 years ago
1
Using the SCTransform integrated "data" slot as corrected counts for downstream pseudotime analysis
#115
lucygarner
closed
2 years ago
1
non-stop when running SCTransform()
#114
zhijunyuu
closed
2 years ago
1
Increasing number of genes used for training the NB model
#113
ashokpatowary
closed
2 years ago
0
Repeat on splced counts same normalization as done on counts
#112
aghr
closed
2 years ago
1
Error in handle_design_parameter: Number of rows in col_data does not match number of columns of data
#111
ghost
closed
2 years ago
3
sctransform batch_var error
#110
lo2811
opened
2 years ago
2
SCT v2 models
#109
saketkc
closed
2 years ago
3
SCTransform Node Stack Overflow Error - one cause (Rfast package)
#108
andrei-stoica26
opened
3 years ago
1
get_residual_var() & get_residuals() do not work on the newest Seurat Object (Seurat_4.0.1)
#107
StefaniAstrologo
closed
3 years ago
3
reference.SCT.model doesn't include the model for "vars.to.regress"
#106
albert-ying
closed
3 years ago
1
When using batch_var, error 'undefined columns selected' in SCTModel_to_vst during FindTransferAnchors
#105
nimne
closed
3 years ago
2
When Sctransform should not be used?
#104
ElyasMo
opened
3 years ago
3
SCTransform: Error with merged datasets
#103
arshiyaakeel
closed
3 years ago
14
diff_mean_test on batch-corrected Seurat object
#102
peterras1985
closed
3 years ago
2
Input to sctansform, scaled UMI counts or direct counts
#101
Bonder-MJ
closed
3 years ago
6
Set filtering of genes to FALSE
#100
HaniJieunKim
closed
3 years ago
4
SCTransform: merge different conditions and /or integration
#99
behyag
closed
2 years ago
1
diff_mean_test() and group sizes
#98
jhb1980
opened
3 years ago
2
vst and batch_var correction does not work
#97
FelixErnst
closed
3 years ago
1
Velocyto
#96
nasiegel88
opened
3 years ago
1
Can I use the value processed by SCTransform to calcuate variance of genes in one cell?
#95
duocang
closed
3 years ago
5
Update on non-UMI data
#94
JuliaP138
opened
3 years ago
7
Why SCTransform converts the gene expression levels to integers or some categorized values?
#93
ElyasMo
closed
3 years ago
1
problem with regressing out rbc genes, not all variables found in seurat object meta data?
#92
jessicook
closed
3 years ago
3
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
Previous
Next