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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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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, 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，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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Can I used BayesPrism to perform deconvolution on the microarray results (e.g., RMA expression values) by the scRNAseq reference? Suppose I take the relative expressions of RMA values and scRNAseq cou…
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Hi,
Thank you very much for putting together this code.
I would like to better understand when Bulk2Space might help versus when there are limits to applicability to Bulk2Space, following a jour…
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I de-convoluted 12 bulk RNA seq samples of brains from mice subjected to stroke. Each brain was separated into two hemispheres (Ipsilateral where ischemia took place and we expect neuronal death and …
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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…