User: fouerghi20

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fouerghi2030
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Posts by fouerghi20

<prev • 27 results • page 1 of 3 • next >
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Normalization before or after merging the samples in Seurat
... I have 4 scRNAseq samples that I create Seurat objects for. I do the QC on each of these samples and then I merge them using the merge function from Seurat. I then normalize, scale, and run PCA on the merged dataset. Then, I take the normalized count matrix from Seurat and input it into Harmony. Do ...
single cell batch effect correction seurat written 10 days ago by fouerghi2030 • updated 10 days ago by jared.andrews078.3k
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Algorithm to remove batch effects
... From your own experience, is it better to do batch effect correction with Seurat (using CCA) or through Harmony (using it through the Seurat Wrappers)? ...
rna-seq batch effect correction single cell written 12 days ago by fouerghi2030
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Comment: C: Is it worth it to explore outside of Seurat?
... Thank you! I will look into OSCA. ...
written 13 days ago by fouerghi2030
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Is it worth it to explore outside of Seurat?
... Is it worth to explore doing single cell analysis outside of Seurat, or is the Seurat package pretty comprehensive for basic analyses? Is it worth it to look into other approaches outside of Seurat for quality control, dimensionality reduction, visualization... and what would the advantages be? Genu ...
single cell seurat written 13 days ago by fouerghi2030 • updated 13 days ago by ATpoint44k
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Answer: A: Labeling Clusters in ggplot
... This is what ended up working for me: data$seurat_clusters <- factor(data$seurat_clusters,labels=c("..","..")) data2 <- data %>% group_by(seurat_clusters) %>% select(tSNE_1, tSNE_2) %>% summarize_all(mean) View(data$seurat_clusters) ggplot(data, aes(tSNE_1,t ...
written 19 days ago by fouerghi2030
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FeaturePlot on a KDE Plot/density plot
... I created a KDE plot (density plot) using the following code: contplus <- data.frame(scADAR$tsne@cell.embeddings) tSNE_1 <- scADAR$tsne@cell.embeddings[,1] tSNE_2 <- scADAR$tsne@cell.embeddings[,2] # Initialize arrays for data subsets for each condition and for plots ...
R single cell seurat rna-seq written 19 days ago by fouerghi2030
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Labeling Clusters in ggplot
... I have a data matrix I extracted from seurat and I want to plot the tSNE plot by using ggplot. I don't know how to label the clusters on the plot with 0..15. Help is appreciated. ...
ggplot single cell written 4 weeks ago by fouerghi2030
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Error when running ssGSEA
... I am trying to ssGSEA on a gct file I created from an expression matrix and I keep getting the following error that halts the execution of ssGSEA: Error in if (max.ES > -min.ES) { : missing value where TRUE/FALSE needed Calls: ssGSEA.cmdline Execution halted Any help on what I can do? ...
ssgsea gsea gene enrichment written 5 weeks ago by fouerghi2030
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Comment: C: Duplicated row names on Seurat
... I found an explanation basically saying that there are gene names that get duplicated because ["there isn't consensus over which coding sequence represents the common name."][1] I made the gene names unique and was able to create the Seurat object while preserving the structure of the matrix. [1 ...
written 5 weeks ago by fouerghi2030
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Duplicated row names on Seurat
... Can you run CCLE data through the Seurat R package? My counts matrix has duplicated feature names, so I can't provide it as an input matrix to CreateSeuratObject() because it only takes matrices with non-duplicated row names (AKA feature names). ...
ccle seurat scrnaseq single cell written 5 weeks ago by fouerghi2030 • updated 17 days ago by Biostar ♦♦ 20

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