scFEA

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scFEA output

8

For the same data, when I work with a smaller number of cells (1000), it works fine. But when I'm working with a lot more cells (>50000),The flux and balance...

niuruize

The practical result differs from the tutorial

1

Hello everyone, why is there such a big difference in the picture I made following the tutorial? 

wenhai-cell87

Balance values interpretation

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As others have indicated previously. It is not clear how to interpret the balance values (especially the negative values). Could you maybe explain it a bit more in simpler terms?

iichelhadi

How to biologically interpret negative flux values?

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hi, everyone, as I can see there are many people have the same question with me, that is what does a negative flux value biologically mean? Did anyone have some...

Joyjoyjoyc

questions about Pandas?

4

(base) C:\Users\Lenovo\scFEA>python src/scFEA.py --data_dir data --input_dir input --test_file Seurat_geneExpr.csv --moduleGene_file module_gene_glutaminolysis1_m23.csv --stoichiometry_matrix cmMat_glutaminolysis1_c17_m23.csv --cName_file cName_glutaminolysis1_c17_m23.csv --output_flux_file output/Seurat_gluta_flux.csv --output_balance_file output/Seurat_gluta_balance.csv Starting load data... Load compound name file, the balance output will...

DylanGuo1101

How to biologically interpret negative flux values

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Hi, I would like to know how to biologically interpret negative flux values? Does this indeed mean that the reaction has reversed? Would you anticipate this to mean that there...

AlisonKennedy

TypeError: can't convert np.ndarray of type numpy.object_. The only supported types are: float64, float32, float16, complex64, complex128, int64, int32, int16, int8, uint8, and bool.

3

Hi, I met a wrong when I run the mouse data. My input data is in .csv format. When it runs into this step, occurred some wrongs. _Starting load data......

QianChwnLyn

AttributeError: 'DataFrame' object has no attribute 'append'. Did you mean: '_append'?

2

when I use the test data Melissa_full.csv to run the code, the below error appear. AttributeError: 'DataFrame' object has no attribute 'append'. Did you mean: '_append'? how do i fixed...

ltgmri

Is there any difference between inputting the count type or normalized expression matrix? What is the recommended data format for single cell analysis (also for bulk RNA-seq data, raw count,...

LiuCanidk

**Thanks for the brilliant scFEA. However, I am running into a problem. The error is as below:** ```Calculated MAGIC in 20.65 seconds. Load compound name file, the balance output will...

pinkrabbit0326