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
Regressing out vars.to.regress takes a very long time for samples with >10k cells
#195
fauxrest
opened
2 weeks ago
0
Integration & Subset
#194
galaxyeee
opened
3 weeks ago
0
SCTransform vars.to.regress Contrasts can be applied only to factors with 2 or more levels
#193
UKECat
opened
1 month ago
0
Issue with calling "glmGamPoi" to work
#192
Joy8Liu
closed
1 month ago
1
failed install of sctransform 0.3.5, but successful install of 0.3
#188
bpyenson
closed
2 months ago
4
Error running on cellbender adjusted counts
#187
yesitsjess
opened
2 months ago
5
Error in make_cell_attr(umi, cell_attr, latent_var, batch_var, latent_var_nonreg, : count matrix must have row and column names
#186
Sunnyxia040103
closed
3 months ago
3
Working back to raw counts from corrected counts?
#185
abussing
closed
3 months ago
3
explanation for the algorithm
#184
BenxiaHu
opened
3 months ago
0
Fix ORCID
#183
dieghernan
closed
4 months ago
1
Workflow for SCTransform and merged samples
#182
Evenlyeven
closed
4 months ago
2
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 'x' must be atomic / sctransform
#180
pstrangw
opened
5 months ago
3
Understanding the purpose of corrected counts
#179
danielcgingerich
closed
5 months ago
2
Obtain expression data for the specific genes on integrated seurat project
#178
jfoedfjwofa
closed
5 months ago
1
ERROR: `assay` must be one of "SCT" or "integrated", not "RNA"
#177
osmanmerdan
closed
7 months ago
1
Hi Alex,
#176
AAA-3
closed
7 months ago
0
Clustering hugely influenced by TCR[A/B/G/D] genes in SCTransform
#175
raunakkar
closed
7 months ago
3
"vars.to.regress" not working
#174
xiao00su
closed
7 months ago
3
How to set n_genes in SCTransform
#173
SihanLiUVa
closed
7 months ago
1
Error in umi@x: no applicable method for `@` applied to an object of class "matrix"
#172
ceesu
closed
9 months ago
1
Update utils.R, make_cell_attr()
#171
moi-taiga
closed
9 months ago
1
Error in umi@x : no applicable method for `@` applied to an object of class "matrix" with v2 regularization
#170
jjia1
closed
10 months ago
9
FindAllMarkers on SCT V1 assay or RNA on a single sample (non-integrated)?
#168
fahmadimoughari
closed
11 months ago
12
SCTransfrom Error in Base Options
#167
ccomo0730
closed
11 months ago
0
TPM input
#166
seongguheo
closed
1 year ago
1
Why $SCT assay during differential expression analysis?
#165
Ryuzaman
closed
1 year ago
2
Using counts from 'SCT' assay and 'data' slot for trajectory analysis
#164
reneemoerkens
closed
1 year ago
1
increase limit of theta.ml when method is default poisson
#163
adugourd
closed
1 year ago
1
Inquiry about the batch correction model
#162
jcho23
opened
1 year ago
0
Correct workflow to perform SCTransform v2 on separate or merged dataset
#161
reneemoerkens
closed
1 year ago
11
Question about a code section in vst(): why are genes with actual_theta/predicted_theta < 0.001 set to theta = Inf
#160
ScreachingFire
closed
1 year ago
2
Questions about errors in the sctransform for selected genes
#158
HelloWorldLTY
closed
1 year ago
1
Sctransform with multiple samples per batch
#157
ConDem94
closed
1 year ago
1
Questions about finding different gene-peak links based on rna and sct (related to sctransform)
#156
HelloWorldLTY
closed
1 year ago
2
Delete get_nz_median, fix usage in get_residuals_var, add unit tests
#155
boomanaiden154
closed
1 year ago
1
Weirdly long and likely unneeded runtimes for get_residuals() and SCTransform(residual_features = [subset of genes])
#154
ScreachingFire
closed
1 year ago
1
Does sctransform support parallelization?
#153
ScreachingFire
closed
1 year ago
3
How to deal with nested effects in scTransform.
#152
AnthoOzier
closed
1 year ago
1
Data visualization and differential gene expression after SCT normalization and integration
#151
yuyuliu
closed
1 year ago
1
Why the difference in sample order affects the sctransform results
#150
yuxuanChen777
opened
1 year ago
3
combining incrementally available data
#149
e-manduchi
closed
1 year ago
2
Please specify Matrix version with equal separation signs
#148
tillea
closed
8 months ago
6
Error in make_cell_attr(umi, cell_attr, latent_var, batch_var, latent_var_nonreg, : cell attribute "log_umi" contains NA, NaN, or infinite value
#146
LooLipin
closed
1 year ago
2
Cannot install sct on macbook pro
#145
shwetajohari
closed
1 year ago
2
Updates to handle Matrix 1.4-2 related changes
#144
saketkc
closed
1 year ago
0
Is the CRAN version v2 now?
#143
alexlenail
closed
1 year ago
1
Calculate counts-per-million from depth-corrected SCTtransformed `v2` counts.
#142
fjrossello
closed
1 year ago
2
SCTransform lapply error
#141
wma316
closed
1 year ago
1
How integrate and rescue full genes in method sctransform
#140
PilanEli
closed
1 year ago
0
Is it OK to use SCTransform on SoupX modified data?
#139
kaizen89
closed
1 year ago
2
Next