wguo-research scCancer issues

wguo-research / scCancer

A package for automated processing of single cell RNA-seq data in cancer

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liger dependency error

#45 nicholas-middelberg opened 2 weeks ago
1
Two doubts, could you please clarify. One, I didn't get plot related with Ambient RNAs contamination fraction estimation. I run the program based on the sample data(KC data) provided in the tutorial. The second doubt is I got some warning messages, after running the scAnnotation module, which is given below

#44 SaleenaYounus opened 3 months ago
3
Error in xtfrm.data.frame(x) : cannot xtfrm data frames

#43 zongfl opened 4 months ago
0
about python module for malignant cell detection mentioned in scCancer2

#42 xflicsu opened 5 months ago
1
ERROR

#41 mabaoweireadingene opened 10 months ago
1
Spatial transcriptomic data compatibilty?

#40 rajeha opened 1 year ago
1
Error in base::colSums(x, na.rm = na.rm, dims = dims, ...) : 'x' must be an array of at least two dimensions

#39 shuaifengwang opened 1 year ago
0
How to set the parameters to generate pdf files?

#38 xxz19900 opened 1 year ago
0
Issues about scCombination

#37 Tianqi-Ma opened 2 years ago
0
Analysis of "cellranger multi" output

#36 HeyLifeHD opened 2 years ago
0
Malignant cell threshold？（malign.thres <- getBimodalThres(scores = obserScore.smooth)？）

#35 khl0798 opened 2 years ago
0
error message during runScAnnotation process "runCellInteraction"

#34 wulc21 opened 2 years ago
2
scCancer installation

#33 Charlesyip2016 opened 2 years ago
0
Dear developers of scCancer, error in Run scAnnotation: [2021-04-25 21:26:54] START: RUN scAnnotation - Warning in 'prepareSeurat': Cannot find the raw data, and use the filtered data instead. [2021-04-25 21:26:54] -----: data preparation Error in `.rowNamesDF<-`(x, value = value) : missing values in 'row.names' are not allowed

#32 Yiquan-Jiang opened 3 years ago
0
issues with RUN scAnnotation

#31 AteeqMKhaliq opened 3 years ago
8
Most difficult to Install

#30 AteeqMKhaliq closed 3 years ago
0
About ambient genes

#29 evenDDDDD opened 3 years ago
1
install error

#28 l-magnificence opened 3 years ago
4
problem with runMalignancy（）

#27 MMriran opened 3 years ago
0
question about runExprProgram（)

#26 MMriran opened 3 years ago
1
Cannot install package using R version = 4.0.3

#25 rrchai opened 3 years ago
1
how to prepare the ` cnv.referAdjMat`

#24 hzongyao opened 3 years ago
1
How to get the infercnv heatmap？

#23 MMriran closed 3 years ago
1
How to use the scCancer with a present Seurat

#22 MMriran opened 4 years ago
1
An error occur when "geneSet.method = "GSVA"" used

#21 dioncst closed 3 years ago
3
Error in plotMarkerDistribution(sc): Failed as no clusters found! Clustering must be set via 'setClusters' to find marker genes.

#20 honghh2018 closed 4 years ago
1
where are the code show on the document you post?

#19 honghh2018 closed 4 years ago
1
在运行cell interaction过程中，错误：没有getCellTypeColor这个函数

#18 Yiquan-Jiang closed 4 years ago
3
Errors about installation

#17 Yiquan-Jiang opened 4 years ago
1
请问这个包只能处理10x的数据吗？现成的矩阵是否可以呢？

#16 Yiquan-Jiang opened 4 years ago
5
Cannot go through scAnnotation and the following scCombination

#15 wiceshine closed 4 years ago
8
Occurred error from install scCancer

#14 honghh2018 opened 4 years ago
1
Error in eval(e, x, parent.frame()) : object 'Type' not found

#13 wiceshine closed 4 years ago
3
Cell QC suggestion

#12 Puriney closed 4 years ago
1
Can we change marker genes used in scatter plots?

#11 dioncst closed 4 years ago
3
I only have a filtered_feature_bc_matrix ,get an error messages

#10 jinyuede closed 4 years ago
1
Use 'data' for estimating ligand-receptor pairs

#9 Puriney opened 4 years ago
1
How scCancer handle the hg19 and hg38 for the interaction score?

#8 Puriney closed 4 years ago
1
New feature request: multimodal data?

#7 lagzxadr closed 4 years ago
4
New Feature request: UMAP

#6 Puriney closed 4 years ago
2
How the gene signatures for TME cell types are curated?

#5 Puriney closed 4 years ago
6
New feature request: Doublet Detection

#4 Puriney closed 4 years ago
3
Description of the reference cells for inferring CNV (cnvRefData-immune.RDS)

#3 Puriney closed 4 years ago
2
Where to put the normal cells for scCancer to run inferCNV

#2 Puriney closed 4 years ago
1
Better picture resolution

#1 HaochenW closed 4 years ago
1