Skip to content

Issues: satijalab/sctransform

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

42 Open 141 Closed
42 Open 141 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Error: make_cell_attr - log_umi contains NA, NaN, or infinite value in SCTransform
#200 opened Nov 6, 2024 by unikill066
1
Regressing out vars.to.regress takes a very long time for samples with >10k cells
#195 opened Jun 17, 2024 by professor-sagittarius
Integration & Subset
#194 opened Jun 13, 2024 by galaxyeee
SCTransform vars.to.regress Contrasts can be applied only to factors with 2 or more levels
#193 opened May 8, 2024 by UKECat
Error running on cellbender adjusted counts
#187 opened Apr 10, 2024 by yesitsjess
5
explanation for the algorithm
#184 opened Mar 16, 2024 by BenxiaHu
Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 'x' must be atomic / sctransform
#180 opened Jan 25, 2024 by pstrangw
@saketkc
3
Inquiry about the batch correction model
#162 opened Apr 4, 2023 by jcho23
Why the difference in sample order affects the sctransform results
#150 opened Oct 24, 2022 by yuxuanChen777
3
Question about Reproducing a Plot in the Paper Introducing the SCTransform (Hafemeister, C., & Satija, R. #1999)
#136 opened Apr 26, 2022 by mcap91
2
batch_var doesn't work with vst.flavor = 'v2'
#126 opened Feb 10, 2022 by cnk113
2
batch_var is not corrected in sctransform::correct
#125 opened Jan 18, 2022 by dg520
Question: Is it possible to reverse the scaling done by vst()? more-information-needed
#122 opened Jan 6, 2022 by TeodoraTockovska
4
'node stack overflow' when using 'IntegrateData'!
#119 opened Dec 16, 2021 by amssljc
1
Selection of the number of cells used for the NB regression in SCTransform
#118 opened Dec 13, 2021 by BiotechPedro
Error when running SCtransform
#117 opened Nov 30, 2021 by KaWingLee9
1
sctransform batch_var error
#110 opened Sep 3, 2021 by lo2811
2
SCTransform Node Stack Overflow Error - one cause (Rfast package)
#108 opened Jun 27, 2021 by andrei-stoica26
1
When Sctransform should not be used?
#104 opened May 7, 2021 by ElyasMo
3
diff_mean_test() and group sizes
#98 opened Mar 18, 2021 by jhb1980
2
Velocyto
#96 opened Feb 22, 2021 by nasiegel88
1
Update on non-UMI data
#94 opened Feb 5, 2021 by JuliaP138
7
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 opened Dec 16, 2020 by connorhknight
11
SCTransform gives 'BLAS/LAPACK routine 'DLASCLS'" error
#85 opened Dec 7, 2020 by spadavec
5
Does sctransform normalisation account for changes in RNA composition?
#83 opened Nov 17, 2020 by lucygarner
1
ProTip! Type g i on any issue or pull request to go back to the issue listing page.