constantAmateur/SoupX
R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
R
Issues
- 0
tar.gz cellranger folders
#161 opened by rbutleriii - 2
autoEstCont error
#126 opened by joe-jhou2 - 0
SoupX error
#160 opened by angelica-varesi - 0
Error converted from warning
#159 opened by Echoloria - 0
plotMarkerMap returns empty plot
#158 opened by Michael-Geuenich - 10
table of droplets (tod) and table of counts (toc) have different numbers of genes
#148 opened by al3xmlt030 - 1
RNA velocity
#152 opened by Sirin24 - 0
- 0
Manually setting contamination fraction
#156 opened by yesitsjess - 0
How to SoupX for analysed data, Seurat object?
#155 opened by mainharryHR - 0
SoupX high contamination guideline
#154 opened by pedriniedoardo - 0
too few genes that passed tf-idf cutoff
#137 opened by wbvguo - 0
Running SoupX on Multiome Data
#153 opened by nic-ghub2 - 0
Extremely high contamination estimated (0.61)
#151 opened by mibdx-dev - 0
Conflicting SoupX results
#150 opened by koushik1989 - 3
autoEstCont error : Error in quantile.default(soupProf$est, soupQuantile) : missing values and NaN's not allowed if 'na.rm' is FALSE
#140 opened by JS0715 - 0
Combining Ambient RNA Methods
#149 opened by Reyhaneh92 - 2
- 1
Cellranger multi compatibility
#138 opened by Nusob888 - 0
Unable to knit when running load10X from SoupX
#147 opened by JasperGattiker - 2
Error running SoupX
#144 opened by malonzm1 - 0
Error: No plausible marker genes found
#146 opened by acv21 - 0
For loops don't seem to work with soupX
#145 opened by Kenneth-new-user - 1
- 0
Filtered data from cellranger
#143 opened by silvainp - 1
Prepare for upcoming Seurat v5 release
#141 opened by saketkc - 0
What types of clustering is required?
#142 opened by JiahuaQu - 1
- 2
autoEstCont() error
#118 opened by Polligator - 0
dd file is empty
#139 opened by dabbas89 - 5
- 1
Using SoupX with non-integer counts
#135 opened by me-orlov - 5
Deprecated method from package "Matrix"
#120 opened by mvfki - 0
- 0
SOUPX for R4.2.2
#133 opened by alessandrapas - 0
Inconsistent cellID in toc and tod
#131 opened by lishuangshuang0616 - 0
other assay compatibility
#130 opened by roosheelpatel - 0
Error in autoestcount
#129 opened by svaidy88 - 0
- 0
- 2
- 10
Issue importing cellranger 7.0.0 outs
#113 opened by ollieeknight - 1
Question about rho_c
#121 opened by Hanxi-002 - 1
Should I run this before or after imputation?
#119 opened by ayeTown - 1
Working with inaccurate cell calling data
#115 opened by RuiyuRayWang - 2
autoEstCont() error in SoupX with CellRanger Data
#116 opened by CTChameleon - 1
plotMarkerMap doubt
#114 opened by MartaSanchezCarbonell - 1
Cell Ranger multi support
#110 opened by gilstel - 1
quickMarkers specify clusters to compare
#109 opened by parkjooyoung99 - 1