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Issues list

How to specify "this gene is only expressed in these cell types" to SoupX .
#167 opened Jan 16, 2025 by alexlenail
3
Soupx for multiplexed samples
#166 opened Jan 7, 2025 by bapoorva
Running SoupX without 10X raw gene by cells matrix
#165 opened Nov 5, 2024 by RunyuXia
1
At which point should I perform ambient RNA correction?
#164 opened Aug 31, 2024 by Chaosli98
1
Correction of ADT tags (protein data) of CITEseq
#163 opened Jul 23, 2024 by tumorscholar
Donor specific ambient RNA
#162 opened Jul 10, 2024 by ramadatta
tar.gz cellranger folders
#161 opened Jun 20, 2024 by rbutleriii
SoupX error
#160 opened Jun 18, 2024 by angelica-varesi
1
Error converted from warning
#159 opened Jun 3, 2024 by Echoloria
2
plotMarkerMap returns empty plot
#158 opened May 31, 2024 by Michael-Geuenich
1
Should I run this before or after dead/dying cell removal?
#157 opened May 17, 2024 by erzakiev
How to SoupX for analysed data, Seurat object?
#155 opened Apr 27, 2024 by mainharryHR
SoupX high contamination guideline
#154 opened Apr 19, 2024 by pedriniedoardo
3
Running SoupX on Multiome Data
#153 opened Apr 12, 2024 by nic-ghub2
RNA velocity
#152 opened Apr 8, 2024 by Sirin24
1
Extremely high contamination estimated (0.61)
#151 opened Apr 5, 2024 by mibdx-dev
Conflicting SoupX results
#150 opened Mar 7, 2024 by koushik1989
Combining Ambient RNA Methods
#149 opened Feb 13, 2024 by Reyhaneh92
table of droplets (tod) and table of counts (toc) have different numbers of genes
#148 opened Feb 7, 2024 by al3xmlt030
10
Unable to knit when running load10X from SoupX
#147 opened Dec 19, 2023 by JasperGattiker
Error: No plausible marker genes found
#146 opened Nov 15, 2023 by acv21
For loops don't seem to work with soupX
#145 opened Nov 14, 2023 by Kenneth-new-user
Error running SoupX
#144 opened Nov 3, 2023 by malonzm1
2
Filtered data from cellranger
#143 opened Oct 25, 2023 by silvainp
What types of clustering is required?
#142 opened Oct 13, 2023 by JiahuaQu
1
ProTip! Updated in the last three days: updated:>2025-02-06.