User: chipolino

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chipolino40
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Posts by chipolino

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Comment: C: scATAC-seq analysis, data preprocessing
... Thanks! But how do you find most variable peaks, if the data is binary? ...
written 9 weeks ago by chipolino40
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Comment: C: scATAC-seq analysis, data preprocessing
... can I do sparse PCA on scATAC-seq matrix and see, what peaks correspond to, let's say the first component? And choose those as the most informative (variable)? ...
written 9 weeks ago by chipolino40
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scATAC-seq analysis, data preprocessing
... Hi, During scATAC-seq data preprocessing, does it make sense to filter data matrix, so it contains only most variable peaks (in the same way how we do it for scRNA-seq), before any further dimensionality reduction or clustering analysis? Thanks ...
scatac-seq written 9 weeks ago by chipolino40 • updated 9 weeks ago by geek_y9.8k
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UMAP interpretation in scRNA-seq analysis
... Hi, If you analyze scRNA-seq data of some differentiation process (like stem cells) and use UMAP to visualize it, can you use the plot to retrieve the actual differentiation trajectory? I know that for example velocyto uses tSNE for this purpose, and UMAP was reported to be better in manifold captu ...
scrna-seq umap pseudotime written 12 weeks ago by chipolino40 • updated 10 weeks ago by Biostar ♦♦ 20
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Comment: C: Distance for gene expression samples
... Thank you for your awesome answer! ...
written 12 weeks ago by chipolino40
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Comment: C: Distance for gene expression samples
... Row z-score is to make sure that genes with higher expression don't have much influence on what samples are similar to each other. I just wanted to make sure that it makes sense and I didn't miss anything ...
written 12 weeks ago by chipolino40
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Comment: C: Distance for gene expression samples
... Well, I do know the basics. And I know that people usually calculate the distance with log CPM. However, my question is about TPM. What did I miss in the basics in your opinion? ...
written 12 weeks ago by chipolino40
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Distance for gene expression samples
... Hi, Imagine I have 200 samples, and for each, I have expression values of 500 genes (so it's a matrix with 500 rows and 200 columns). Expression values are normalized, it’s TPM. I need to compute a distance between the samples. What is the better way of doing it? Should I take log(TPM+1), then scal ...
rna-seq distance written 12 weeks ago by chipolino40 • updated 12 weeks ago by Kevin Blighe45k
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Drug target discovery with single cell RNA-seq
... Hi everyone! Suppose, I have single cell RNA-seq data with two time points: cells at zero time point that are not treated by some drug, cells after the drug treatment. My goal is to identify a mechanism of action of this drug (its targets). Is there any good way of how I can do it? I was thinking a ...
scrna-seq drug target written 6 months ago by chipolino40 • updated 4 months ago by Biostar ♦♦ 20
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mitochondrial/ribosomal protein genes in scRNA-seq analysis
... Hi everyone, According to this [tutorial][1], during the first steps of scRNA-seq analysis (normalization, dimensionality reduction, and finding DE genes), you should remove all mitochondrial/ribosomal protein genes. But I also heard from other experts that it's a bad idea and you should not do i ...
scrna-seq data processing rna-seq written 6 months ago by chipolino40

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