wu-yc scMetabolism issues

wu-yc / scMetabolism

Quantifying metabolism activity at the single-cell resolution

BSD 3-Clause "New" or "Revised" License

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Error: (converted from warning) 'as(<matrix>, "dgeMatrix")' is deprecated. Use 'as(as(as(., "dMatrix"), "generalMatrix"), "unpackedMatrix")' instead.

#34 Noralii opened 1 day ago
0
DotPlot.metabolism(obj = countexp.Seurat, pathway = input.pathway, phenotype = "ident", norm = "y")", Error in [.data.frame(metadata, , input.parameter) : 选择了未定义的列

#33 foelen closed 1 month ago
0
Installation fails due to failure of dependency VISION (which is due to loe)

#32 bbimber opened 1 month ago
3
How

#31 gengbaobao closed 1 month ago
0
Error in if (class(A_norm) != "matrix") { : the condition has length > 1 此外: Warning message: In asMethod(object) : sparse->dense coercion: allocating vector of size 5.9 GiB

#30 Xxian10 opened 2 months ago
0
Error in if (tolower(filter) == "novar") { : missing value where TRUE/FALSE needed In addition: Warning messages: 1: In asMethod(object) : sparse->dense coercion: allocating vector of size 21.9 GiB 2: In readSignaturesInput(signatures) : NAs introduced by coercion

#29 ltgmri opened 4 months ago
1
Fix issue when reduction uses a different key

#28 bbimber closed 3 weeks ago
1
uncompatible packages for install scMetabolism

#27 ZixuanEYE opened 5 months ago
3
Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.

#26 EvaChung6 opened 5 months ago
6
Error in data.frame(C = consistency, pValue = pvals, FDR = fdr) : arguments imply differing number of rows: 1, 0

#25 wchenqi opened 9 months ago
2
Would it be possible to access to the .cloupe files in the study?

#24 jiazhen-rong closed 9 months ago
2
Update compute_metabolism.R

#23 Biocxifu opened 1 year ago
0
Update compute_metabolism_Seurat.R

#22 Biocxifu opened 1 year ago
0
Error in "Computing differential signature tests..." step

#21 JunyanKan opened 1 year ago
3
What does the negative values in the result mean?

#20 Pang-Ka opened 1 year ago
0
DimPlot.metabolism function

#19 joe-jhou2 opened 1 year ago
1
Error: as(, "dgeMatrix") is deprecated since Matrix 1.5-0; do as(as(as(., "dMatrix"), "generalMatrix"), "unpackedMatrix") instead

#18 XuenaXie opened 1 year ago
4
sc.metabolism.Seurat/sc.metabolism returns error

#17 goterm closed 1 year ago
14
About cell type annotation of your paper.

#16 BinDuan closed 1 year ago
0
how to deal with batcheffect if the analysis needs to be done on raw count data?

#15 ygz605500160 opened 1 year ago
1
Error: as(<matrix>, "dgeMatrix") is deprecated since Matrix 1.5-0;

#14 luohaohao opened 1 year ago
5
Update compute_metabolism.R

#13 zerostwo opened 1 year ago
0
Error in sc.metabolism.Seurat

#12 longLabzj closed 1 year ago
1
The devtools::install_github("YosefLab/VISION") need package phanghorn but not the package found in CRAN

#11 honghh2018 opened 2 years ago
0
gsva method in sc.metabolism.Seurat

#10 hjames1 opened 2 years ago
0
Errors when running sc.metabolism.Seurat using ssgsea/gsea

#9 Jonathanyu2014 closed 2 years ago
1
input data type

#8 williamhsy closed 2 years ago
1
how to handle large dataset(>65000 cells) in scMetabolism?

#7 ybyOxidant opened 2 years ago
5
question about DotPlot.metabolism

#6 xutongran closed 2 years ago
1
Adaptation for mouse data

#5 jdarmitage closed 2 years ago
2
Data access

#4 chsher closed 2 years ago
1
which cells to choose as input when studying difference between subtypes

#3 chengwenxuan1997 closed 2 years ago
1
BoxPlot.metabolism issue, obj not in function code

#2 msalaciak opened 2 years ago
5
Some questions about the applications of scRNAseq to metabolism.

#1 xiaozhongshen closed 2 years ago
3