User: asyndeton17

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asyndeton1720
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Posts by asyndeton17

<prev • 15 results • page 1 of 2 • next >
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Comment: C: Making a 3d tSNE Plot in Seurat for scRNA-seq
... Is there a way to do so with another package? ...
written 20 months ago by asyndeton1720
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Making a 3d tSNE Plot in Seurat for scRNA-seq
... Hi, Is there an easy way to make a 3D tSNE plot of the single cell clusters in Seurat? Thanks ...
scrna-seq tsne rna-seq seurat written 20 months ago by asyndeton1720 • updated 18 months ago by garyhokawai30
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Comment: C: edgeR RNA-seq Results Across Conditions
... For the most part, I am following the Griffith Lab Tutorial: https://github.com/griffithlab/rnaseq_tutorial/blob/master/scripts/Tutorial_Module4_Part4_edgeR.R ...
written 21 months ago by asyndeton1720
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Comment: C: edgeR RNA-seq Results Across Conditions
... Would it work if I filtered lowly expressed counts before creating the edgeR object? If so, what sort of cutoff should I make? ...
written 21 months ago by asyndeton1720
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edgeR RNA-seq Results Across Conditions
... Hi, I recently performed RNA-seq differential expression analysis. I first did a comparison between Condition 2 vs. Control. Then I did Condition 3 vs. Control. However, the raw counts do not seem to be substantiating the output data from edgeR. For instance, the Krt17 gene supposedly has a log fol ...
rna-seq edger written 21 months ago by asyndeton1720 • updated 21 months ago by shoujun.gu370
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Comment: C: Finding Variable Genes in Seurat, scRNA-seq
... Yes, the help page for the function says to examine "the plot" first, but it doesn't refer to which plot. ...
written 21 months ago by asyndeton1720
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Finding Variable Genes in Seurat, scRNA-seq
... Hi, I have a data matrix for scRNA-seq data (Drop-seq). How do I choose the parameters appropriately for the FindVariableGenes function in Seurat? Is there a plot I should be looking at beforehand to determine the correct parameters? I can provide plots if needed. Thanks ...
scrna-seq rna-seq seurat written 21 months ago by asyndeton1720 • updated 4 months ago by Nitin Sharma30
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Comment: C: Combining Conditions in scRNA-seq (Drop-seq) for Analysis
... That seems reasonable. Will I be able to keep track of which condition cells came from within the matrix? If so, how? ...
written 21 months ago by asyndeton1720
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Comment: C: Combining Conditions in scRNA-seq (Drop-seq) for Analysis
... Yes, there are many cells for each condition, but I want to plot both conditions onto one plot (probably a PCA plot). ...
written 21 months ago by asyndeton1720
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Combining Conditions in scRNA-seq (Drop-seq) for Analysis
... Hi, I recently ran a Drop-seq experiment and got my demultiplexed data back for two different conditions. When should I combine the two files together? I began with two queryname-sorted BAM files. Should I merge the files after alignment, right before alignment, or after I extract the matrix for ea ...
scrna-seq drop-seq rna-seq written 21 months ago by asyndeton1720 • updated 21 months ago by Devon Ryan90k

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