constantAmateur SoupX issues

constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

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issues

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Cell level Rho values are the same in the whole dataset

#61 yunguan-wang closed 3 years ago
1
How to proceed when "Extremely high contamination estimated"?

#60 gene-drive closed 3 years ago
2
Running autoEstCont() gets error message

#59 mouni521 closed 3 years ago
3
Further vignette fixes.

#58 constantAmateur closed 3 years ago
0
Fix links in vignette.

#57 constantAmateur closed 3 years ago
0
Devel

#56 constantAmateur closed 3 years ago
0
autoEstCont always reduces estimation

#55 kjrgreen1 closed 3 years ago
1
Spurious DEGs introduced by SoupX?

#54 miscellaneousj closed 3 years ago
1
Error correcting expression profile using adjustCounts

#53 fhermans27 closed 3 years ago
6
Loading data and downstream steps

#52 Nur-Taz closed 3 years ago
2
Request for users to specify more ggplot arguments

#51 yu-tong-wang closed 3 years ago
1
Counts 0 and soupest NaN during autoEstCont

#50 jamrute closed 3 years ago
2
Installation failure with STAN

#49 petervangalen closed 3 years ago
1
Suggest formatR because of the chunk option tidy=TRUE in the vignette

#48 yihui closed 4 years ago
0
Presence of ambient RNA after correction ?

#47 akramdi closed 3 years ago
6
Estimating and adjusting counts in soupx

#46 rubinaasharmaa closed 4 years ago
4
Error loading 10x data

#45 anaccsilva closed 4 years ago
6
Opinion on analysis: (1) Auto/Manual; and (2) Before/After doublet removal

#44 nicodemus88 closed 4 years ago
5
Devel

#43 constantAmateur closed 4 years ago
0
Setting optimum threshold for contamination

#42 tomthomas300 closed 3 years ago
1
Is the tutorial is out of date?

#41 I-Hao closed 4 years ago
1
Performance on 10X v3 libraries

#40 jpreall closed 4 years ago
1
Why do I get contamination fraction >100%

#39 chansigit closed 4 years ago
1
Estimated global contamination fraction and cluster info

#38 jmzvillarreal closed 4 years ago
1
load count matrix

#37 icanwinwyz closed 4 years ago
1
Is it possible to add a batch parameter?

#36 kaizen89 closed 4 years ago
1
PlotMarkerDistribution Error

#35 deevdevil88 closed 4 years ago
4
Fix matrix subsetting in expandClusters

#34 gtca closed 4 years ago
1
How SoupX remove ambient RNA expression when two or more gene sets are used?

#33 YiweiNiu closed 4 years ago
1
Estimating the contamination fraction without biological assumptions using Cell Ranger's default clustering results or ERCC spike-ins

#32 vertesy closed 4 years ago
2
Can we compute soup components and adjustCounts separately?

#31 JPingLin closed 4 years ago
1
Problem running on jupyter notebook

#30 alexmascension closed 4 years ago
3
Devel

#29 constantAmateur closed 4 years ago
0
why calling estimateSoup explicitly

#28 chansigit closed 4 years ago
1
\rho_c MLE deriviation

#27 chansigit closed 4 years ago
2
plotMarkerDistribution(sc) error

#26 chansigit closed 4 years ago
2
[Question] Is it possible to feed data into a SoupChannel list besides by using Read10X Function?

#25 cswoboda closed 4 years ago
1
[Question] Using soupX together with doublet detection tools

#24 JonathanCruard closed 4 years ago
2
decontaminating pancreatic dataset

#23 jmzvillarreal closed 4 years ago
1
Error when running calculateContaminationFraction with cellSpecificEstimates = True

#22 rtvest closed 4 years ago
1
multtest not available for R version 3.6.0

#21 cswoboda closed 4 years ago
2
Error in inferNonExpressedGenes(scl) : could not find function "inferNonExpressedGenes"

#20 molybdenumt closed 4 years ago
3
undesirable behavior reading in aggregated 10X data

#19 ONeillMB1 closed 4 years ago
1
[Question] The way to choose soup specific genes

#18 hanbyulcho closed 4 years ago
1
Error with CreateCleanedSeurat function

#17 immune-sc closed 4 years ago
6
Error while running strainCells

#16 shr9st9 closed 4 years ago
1
Loading Data using load10X function

#15 cswoboda closed 4 years ago
0
NaNs in soupMatrix with custom count matrix

#14 SNRNS closed 4 years ago
7
Usage with alevin output

#13 alexvpickering closed 5 years ago
1
Removal of general contaminants

#12 Osynchronika closed 4 years ago
1

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