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Hello,
I very much enjoyed your paper and thank you for your efforts at making an application for deconvolution of bulk RNA-seq available. I have great interest in giving it a shot with my dataset.…
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Can I used for tumor-only bulk mRNA-seq?
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Thanks for the useful deconvolution tool. I am trying to use TED to deconvolute bulk RNA-seq data from tissues. And I used raw reads for scRNA-seq and expected counts generated from RSEM for bulk RNA-…
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Hi @xuranw
I am new to single-cell analysis, would be interested to use music to perform imputation using bulk rna-seq data. I would be using publicly available single-cell datasets.
One challeng…
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Hi, thanks for the nice paper and code.
As I understand it, the decoder function reconstructs the bulk RNA-seq input B from X (the predicted cell fractions). The learnt weights of the decoder func…
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Hi,
I'm learning how to use MuSiC2. When I'm running the sample code in tutorial, an error happened to me. So, how to deal it.
///
> # music2 deconvolution
> set.seed(1234)
> est.prop = MuSiC2:…
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Hi,Thank you for your excellent package for deconvolution analysis; I run into the following error, Do you have any hints to solve this issue?
```
GSE134347.ens
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hello,everyone, I run my code as follow:
library(MuSiC2)
library(MuSiC)
library(bseqsc)
setwd("D:/cibersortx/Music/music2")
## Bulk RNA-seq data
benchmark.eset = readRDS("bulk-eset.rds")
benchm…
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Hi,
I tried ingest using the reference made with BBKNN. As @ivirshup said, ingest was worked by adding `adata_ref.uns['neighbors']['params']['metric'] = 'euclidean'`. However, the result was quite po…
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Hi,
I was wondering if there is a way to estimate the proportion of cells that aren't present in the reference cells? I've deconvoluted bulk RNA-seq data for a tumour with a reference atlas from t…