ecotyper

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Hi Team, I used CODEFACS for deconvolution and trying to use its output as an input for Ecotyper using tutorial_6. As recommended I used all the genes and their deconvolved...

biobug16

Problem step 8

4

Good day! Thanks for developing this wonderful tool. I am trying to use it on my own scRNA-seq data, and did a trial run before, and work nicely. However, with...

ccruizm

problems in tutorial 1

1

Hi, When using the "bulk_lung_data. txt" to run "recovery", we select "Carcinoma", there is an error: "Error in read.table(file = file, header = header, sep = sep, quote = quote,...

lzz-123

could the ecotyper apply to the microarray data directly?

1

According to analysis tutorial, EcoTyper takes as input a bulk gene expression table from RNA-seq or microarray data with the following formatting requirements: Data values can be TPM, FPKM, log2(TPM),...

lzz-123

bulk recovery questions

1

dear EcoTyper team， When we run the bulk data with our own single-cell ‘discovery’ data, there are a total of five hundred samples, and finally only a few cases are...

zhangch365

error in 'Tutorial 1'

1

dear Ecotyper team， We've got our own sc-ecotyper, but when we used the bulk data to recovery it, it reported the following error, 'Error in (function (classes, fdef, mtable) :...

zhangch365

The differences of Tutorial 2 with Tutorial 5

1

Dear EcoTyper team, We want to use ecotyper in our scRNA-Seq dataset. But I was confused with the differences of Tutorial 2 with Tutorial 5. Which analysis pipeline should I...

QianhuiXu

recovery our custom discovery have a problem

3

Hi, When using bulk data to run "recovery", we select "Carcinoma", no error will be reported. But when we use the same bulk data to run "recovery" our custom discovery,...

Eve12126

Question about rank value selection

2

I try to repeat Tutorial 5,with the data you gave,but I found that the final rank value selection (rank_plot.png)is not the same as the one given in your tutorial. Is...

hahahah-single

question regarding abundance table

2

Hi, I am wandering what does the abundance table exactly refer to, is it abundance of cell states among each cell type or is it among all cells. On my...

kaizen89