Ecosyste.ms: Issues

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GitHub / satijalab/sctransform issues and pull requests

#203 - Concern regarding method use for Xenium data

Issue - State: open - Opened by LPotter21 2 months ago - 2 comments

#202 - Error: cannot allocate vector of size 80.7 Gb

Issue - State: open - Opened by mylenaortiz 3 months ago - 2 comments

#201 - Consider standard lapply when there is no parallel processing

Issue - State: closed - Opened by jgarthur 3 months ago - 2 comments

#199 - Converting `scale.data` layer for scTransform to sparce matrix

Issue - State: closed - Opened by siegelna 4 months ago - 2 comments

#198 - scTransform failed without giving errors

Issue - State: closed - Opened by jingsday 7 months ago - 1 comment

#194 - Integration & Subset

Issue - State: open - Opened by galaxyeee 8 months ago

#192 - Issue with calling "glmGamPoi" to work

Issue - State: closed - Opened by Joy8Liu 10 months ago - 3 comments

#188 - failed install of sctransform 0.3.5, but successful install of 0.3

Issue - State: closed - Opened by bpyenson 10 months ago - 4 comments

#187 - Error running on cellbender adjusted counts

Issue - State: open - Opened by yesitsjess 10 months ago - 5 comments

#185 - Working back to raw counts from corrected counts?

Issue - State: closed - Opened by abussing 11 months ago - 3 comments

#184 - explanation for the algorithm

Issue - State: open - Opened by BenxiaHu 11 months ago

#183 - Fix ORCID

Pull Request - State: closed - Opened by dieghernan 12 months ago - 1 comment

#182 - Workflow for SCTransform and merged samples

Issue - State: closed - Opened by Evenlyeven 12 months ago - 2 comments

#179 - Understanding the purpose of corrected counts

Issue - State: closed - Opened by danielcgingerich about 1 year ago - 2 comments

#178 - Obtain expression data for the specific genes on integrated seurat project

Issue - State: closed - Opened by jfoedfjwofa about 1 year ago - 1 comment

#177 - ERROR: `assay` must be one of "SCT" or "integrated", not "RNA"

Issue - State: closed - Opened by osmanmerdan about 1 year ago - 1 comment

#176 - Hi Alex,

Issue - State: closed - Opened by AAA-3 about 1 year ago

#175 - Clustering hugely influenced by TCR[A/B/G/D] genes in SCTransform

Issue - State: closed - Opened by raunakkar about 1 year ago - 3 comments

#174 - "vars.to.regress" not working

Issue - State: closed - Opened by xiao00su about 1 year ago - 3 comments

#173 - How to set n_genes in SCTransform

Issue - State: closed - Opened by SihanLiUVa over 1 year ago - 1 comment

#171 - Update utils.R, make_cell_attr()

Pull Request - State: closed - Opened by moi-taiga over 1 year ago - 1 comment

#167 - SCTransfrom Error in Base Options

Issue - State: closed - Opened by ccomo0730 over 1 year ago

#166 - TPM input

Issue - State: closed - Opened by seongguheo over 1 year ago - 1 comment

#165 - Why $SCT assay during differential expression analysis?

Issue - State: closed - Opened by Ryuzaman almost 2 years ago - 2 comments

#164 - Using counts from 'SCT' assay and 'data' slot for trajectory analysis

Issue - State: closed - Opened by reneemoerkens almost 2 years ago - 1 comment

#163 - increase limit of theta.ml when method is default poisson

Issue - State: closed - Opened by adugourd almost 2 years ago - 1 comment

#162 - Inquiry about the batch correction model

Issue - State: open - Opened by jcho23 almost 2 years ago

#161 - Correct workflow to perform SCTransform v2 on separate or merged dataset

Issue - State: closed - Opened by reneemoerkens almost 2 years ago - 11 comments

#158 - Questions about errors in the sctransform for selected genes

Issue - State: closed - Opened by HelloWorldLTY about 2 years ago - 1 comment

#157 - Sctransform with multiple samples per batch

Issue - State: closed - Opened by ConDem94 about 2 years ago - 1 comment

#155 - Delete get_nz_median, fix usage in get_residuals_var, add unit tests

Pull Request - State: closed - Opened by boomanaiden154 about 2 years ago - 1 comment

#153 - Does sctransform support parallelization?

Issue - State: closed - Opened by ScreachingFire about 2 years ago - 3 comments

#152 - How to deal with nested effects in scTransform.

Issue - State: closed - Opened by AnthoOzier about 2 years ago - 1 comment

#150 - Why the difference in sample order affects the sctransform results

Issue - State: open - Opened by yuxuanChen777 over 2 years ago - 3 comments

#149 - combining incrementally available data

Issue - State: closed - Opened by e-manduchi over 2 years ago - 2 comments

#148 - Please specify Matrix version with equal separation signs

Issue - State: closed - Opened by tillea over 2 years ago - 6 comments

#145 - Cannot install sct on macbook pro

Issue - State: closed - Opened by shwetajohari over 2 years ago - 2 comments

#144 - Updates to handle Matrix 1.4-2 related changes

Pull Request - State: closed - Opened by saketkc over 2 years ago

#143 - Is the CRAN version v2 now?

Issue - State: closed - Opened by alexlenail over 2 years ago - 1 comment

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

Issue - State: closed - Opened by fjrossello over 2 years ago - 2 comments

#141 - SCTransform lapply error

Issue - State: closed - Opened by wma316 over 2 years ago - 1 comment

#140 - How integrate and rescue full genes in method sctransform

Issue - State: closed - Opened by PilanEli over 2 years ago

#139 - Is it OK to use SCTransform on SoupX modified data?

Issue - State: closed - Opened by kaizen89 over 2 years ago - 2 comments

#138 - Doubt Integratedata using normalization SCTransform

Issue - State: closed - Opened by PilanEli over 2 years ago - 3 comments

#137 - Difference between sctransform::vst() and SCTransform()?

Issue - State: closed - Opened by micw42 over 2 years ago - 7 comments

#135 - Cannot install on arm64

Issue - State: closed - Opened by skilpinen almost 3 years ago - 2 comments

#133 - sctransform install; cannot find -lgfortran

Issue - State: closed - Opened by PiaoyangGuohai1 almost 3 years ago - 1 comment

#132 - do.scale = FALSE leads to many subpopulations in UMAP

Issue - State: closed - Opened by george-hall-ucl almost 3 years ago - 4 comments

#130 - Error in h(simpleError(msg, call))

Issue - State: closed - Opened by jiayiliujiayi almost 3 years ago - 2 comments

#129 - prepSCTFindMarkers data correction increased the fraction of zero values.

Issue - State: closed - Opened by yamajackr almost 3 years ago - 2 comments

#128 - scale_factor

Issue - State: closed - Opened by z5ouyang almost 3 years ago - 2 comments

#127 - Default clipping value: sqrt(n_cells/30) or sqrt(n_cells)?

Issue - State: closed - Opened by dkobak almost 3 years ago - 1 comment

#126 - batch_var doesn't work with vst.flavor = 'v2'

Issue - State: open - Opened by cnk113 about 3 years ago - 2 comments

#125 - batch_var is not corrected in sctransform::correct

Issue - State: open - Opened by dg520 about 3 years ago

#124 - variable.features.n didn't change the number of genes used

Issue - State: closed - Opened by Evenlyeven about 3 years ago - 1 comment

#123 - Develop patch 1

Pull Request - State: closed - Opened by rsatija about 3 years ago

#122 - Question: Is it possible to reverse the scaling done by vst()?

Issue - State: open - Opened by TeodoraTockovska about 3 years ago - 4 comments
Labels: more-information-needed

#121 - Function future_lapply is using the default value 'future.seed = FALSE'

Issue - State: closed - Opened by adRn-s about 3 years ago - 3 comments

#120 - Reproducible SCTransform crash

Issue - State: closed - Opened by ms3389 about 3 years ago - 5 comments

#119 - 'node stack overflow' when using 'IntegrateData'!

Issue - State: open - Opened by amssljc about 3 years ago - 1 comment

#117 - Error when running SCtransform

Issue - State: open - Opened by kelvinlee760948065 about 3 years ago - 1 comment

#116 - Missing expm1?

Issue - State: closed - Opened by knokknok over 3 years ago - 1 comment

#114 - non-stop when running SCTransform()

Issue - State: closed - Opened by zhijunyuu over 3 years ago - 1 comment

#112 - Repeat on splced counts same normalization as done on counts

Issue - State: closed - Opened by aghr over 3 years ago - 1 comment

#110 - sctransform batch_var error

Issue - State: open - Opened by lo2811 over 3 years ago - 2 comments

#109 - SCT v2 models

Pull Request - State: closed - Opened by saketkc over 3 years ago - 3 comments

#108 - SCTransform Node Stack Overflow Error - one cause (Rfast package)

Issue - State: open - Opened by andrei-stoica26 over 3 years ago - 1 comment

#106 - reference.SCT.model doesn't include the model for "vars.to.regress"

Issue - State: closed - Opened by albert-ying almost 4 years ago - 1 comment

#104 - When Sctransform should not be used?

Issue - State: open - Opened by ElyasMo almost 4 years ago - 3 comments

#103 - SCTransform: Error with merged datasets

Issue - State: closed - Opened by arshiyaakeel almost 4 years ago - 14 comments

#102 - diff_mean_test on batch-corrected Seurat object

Issue - State: closed - Opened by peterras1985 almost 4 years ago - 2 comments

#101 - Input to sctansform, scaled UMI counts or direct counts

Issue - State: closed - Opened by Bonder-MJ almost 4 years ago - 6 comments

#100 - Set filtering of genes to FALSE

Issue - State: closed - Opened by HaniJieunKim almost 4 years ago - 4 comments

#99 - SCTransform: merge different conditions and /or integration

Issue - State: closed - Opened by behyag almost 4 years ago - 1 comment