satijalab/sctransform

Issues

• scTransform failed without giving errors

  #198 opened 2 months ago by jingsday
  1

• how to run sctransform in python on h5ad UMI matrix count?

  #197 opened 3 months ago by winner0809
  0

• how to run sctransform directly on a h5ad UMI matrix in python?

  #196 opened 3 months ago by winner0809
  0

• Issue with calling "glmGamPoi" to work

  #192 opened 4 months ago by Joy8Liu
  3

• Regressing out vars.to.regress takes a very long time for samples with >10k cells

  #195 opened 3 months ago by professor-sagittarius
  0

• Error running on cellbender adjusted counts

  #187 opened 6 months ago by yesitsjess
  5

• Integration & Subset

  #194 opened 4 months ago by galaxyeee
  0

• Understanding the purpose of corrected counts

  #179 opened 8 months ago by danielcgingerich
  2

• SCTransform vars.to.regress Contrasts can be applied only to factors with 2 or more levels

  #193 opened 5 months ago by UKECat
  0

• failed install of sctransform 0.3.5, but successful install of 0.3

  #188 opened 6 months ago by bpyenson
  4

• Error in make_cell_attr(umi, cell_attr, latent_var, batch_var, latent_var_nonreg, : count matrix must have row and column names

  #186 opened 6 months ago by Sunnyxia040103
  3

• Working back to raw counts from corrected counts?

  #185 opened 6 months ago by abussing
  3

• Workflow for SCTransform and merged samples

  #182 opened 7 months ago by Evenlyeven
  2

• explanation for the algorithm

  #184 opened 6 months ago by BenxiaHu
  0

• Error in sort.int(x, na.last = na.last, decreasing = decreasing, ...) : 'x' must be atomic / sctransform

  #180 opened 8 months ago by pstrangw
  3

• Obtain expression data for the specific genes on integrated seurat project

  #178 opened 8 months ago by jfoedfjwofa
  1

• Clustering hugely influenced by TCR[A/B/G/D] genes in SCTransform

  #175 opened 10 months ago by raunakkar
  3

• Hi Alex,

  #176 opened 10 months ago by AAA-3
  0

• ERROR: `assay` must be one of "SCT" or "integrated", not "RNA"

  #177 opened 10 months ago by osmanmerdan
  1

• "vars.to.regress" not working

  #174 opened 10 months ago by xiao00su
  3

• How to set n_genes in SCTransform

  #173 opened a year ago by SihanLiUVa
  1

• Please specify Matrix version with equal separation signs

  #148 opened a year ago by tillea
  6

• Error in umi@x: no applicable method for `@` applied to an object of class "matrix"

  #172 opened a year ago by ceesu
  1

• Error in umi@x : no applicable method for `@` applied to an object of class "matrix" with v2 regularization

  #170 opened a year ago by jjia1
  9

• FindAllMarkers on SCT V1 assay or RNA on a single sample (non-integrated)?

  #168 opened a year ago by fahmadimoughari
  12

• SCTransfrom Error in Base Options

  #167 opened a year ago by ccomo0730
  0

• TPM input

  #166 opened a year ago by seongguheo
  1

• Why $SCT assay during differential expression analysis?

  #165 opened a year ago by Ryuzaman
  2

• Using counts from 'SCT' assay and 'data' slot for trajectory analysis

  #164 opened a year ago by reneemoerkens
  1

• increase limit of theta.ml when method is default poisson

  #163 opened a year ago by adugourd
  1

• Why the difference in sample order affects the sctransform results

  #150 opened 2 years ago by yuxuanChen777
  3

• Correct workflow to perform SCTransform v2 on separate or merged dataset

  #161 opened 2 years ago by reneemoerkens
  11

• Inquiry about the batch correction model

  #162 opened a year ago by jcho23
  0

• Is it OK to use SCTransform on SoupX modified data?

  #139 opened 2 years ago by kaizen89
  2

• Question about a code section in vst(): why are genes with actual_theta/predicted_theta < 0.001 set to theta = Inf

  #160 opened 2 years ago by ScreachingFire
  2

• How to deal with nested effects in scTransform.

  #152 opened 2 years ago by AnthoOzier
  1

• Questions about errors in the sctransform for selected genes

  #158 opened 2 years ago by HelloWorldLTY
  1

• Sctransform with multiple samples per batch

  #157 opened 2 years ago by ConDem94
  1

• Questions about finding different gene-peak links based on rna and sct (related to sctransform)

  #156 opened 2 years ago by HelloWorldLTY
  2

• Weirdly long and likely unneeded runtimes for get_residuals() and SCTransform(residual_features = [subset of genes])

  #154 opened 2 years ago by ScreachingFire
  1

• Does sctransform support parallelization?

  #153 opened 2 years ago by ScreachingFire
  3

• Data visualization and differential gene expression after SCT normalization and integration

  #151 opened 2 years ago by yuyuliu
  1

• combining incrementally available data

  #149 opened 2 years ago by e-manduchi
  2

• 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 opened 2 years ago by LooLipin
  2

• Cannot install sct on macbook pro

  #145 opened 2 years ago by shwetajohari
  2

• Is the CRAN version v2 now?

  #143 opened 2 years ago by alexlenail
  1

• Calculate counts-per-million from depth-corrected SCTtransformed `v2` counts.

  #142 opened 2 years ago by fjrossello
  2

• SCTransform lapply error

  #141 opened 2 years ago by wma316
  1

• Doubt Integratedata using normalization SCTransform

  #138 opened 2 years ago by PilanEli
  3

• How integrate and rescue full genes in method sctransform

  #140 opened 2 years ago by PilanEli
  0