User: biostarukha

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biostarukha10
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Posts by biostarukha

<prev • 25 results • page 1 of 3 • next >
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Comment: C: How to use DEGs file for GSEA?
... thank you, I understand that now. So, I think I should use average expressions of all genes across clusters and treat them as if they were samples in bulk RNA GSEA. If I understand correctly, in bulk GSEA there should be disease and normal samples. But in scRNA-seq cluster marker genes are usually f ...
written 8 weeks ago by biostarukha10
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Comment: C: GSEA for scRNA-seq
... I have seen in scRNA-seq analysis papers that the authors filtered out insignificant DEGs. For example, this [Nature publication][1]: > DEGs were ranked for gene-set enrichment analysis (GSEA) according to: rank=−10×log10(padj)×sgn[log2(foldchange)]. A subset of 784 housekeeping genes related to ...
written 8 weeks ago by biostarukha10
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Comment: C: GSEA for scRNA-seq
... thank you very much for your comment. So, if I want to use GSEA and compare enrichment across clusters, I basically should input the average expression of all genes per cluster, right? ...
written 8 weeks ago by biostarukha10
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Comment: C: How to use DEGs file for GSEA?
... Thank you for your comment. If I use log2FC of the DEGs without p-value restriction, how can I ensure the significance of the results? There are some high logFC values in my data that also have a very high adj p-value. Also, how do I impute values for those DEGs that absent in some clusters? ...
written 8 weeks ago by biostarukha10
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(Closed) GSEA for scRNA-seq
... I want to run GSEA on my scRNA-seq data using cluster markers. I want to compare enrichment scores for gene sets and pathways **across clusters** in my data. I used Seurat FindAllMarkers to find DEGs for each cluster (cluster of interest vs all remaining cells). For GSEA, I want to use only DEGs wit ...
scrna-seq gsea seurat written 8 weeks ago by biostarukha10
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How to use DEGs file for GSEA?
... I want to run GSEA on my DEGs from scRNA-seq analysis, which contains gene name, logFC, p-value, adjusted p-value data. However, in the Broad Institute GSEA tutorial on how to format input files, their file contains gene expression across multiple samples but not DEGs. Is there any way to use DEGs ...
scrna-seq gsea rna-seq seurat written 8 weeks ago by biostarukha10 • updated 8 weeks ago by rpolicastro4.0k
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Reading count martix in scanpy
... I am trying to read cellranger count matrix using scanpy. The folder 100PDXT contains matrix.mtx.gz, barcodes.tsv.gz, and features.tsv.gz 100PDXT=sc.read_10x_mtx("~/100PDXT/") when I call 100PDXT.obs, I see cell names, but the shape is 3153 rows × 0 columns. AAACCCAAGACCATAA-1 AAACCC ...
scrna-seq python scanpy seurat written 3 months ago by biostarukha10
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Answer: A: Merging previously merged object in Seurat
... Well, I found the solution. Clustering creates seurat_clusters column in metadata and it messes up with a previous seurat_clusters came from cluster1 and cluster3. So, after merging cluster1 and cluster3, I renamed the seurat_clusters column to 'status' clusters1_3@meta.data$status <- cluste ...
written 3 months ago by biostarukha10
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Merging previously merged object in Seurat
... I have two Seurat objects that were made by merging of samples: object1 <-merge(A, y=B, add.cell.ids=c("A","B")) object2 <-merge(C, y=D, add.cell.ids=c("C","D")) For each object I did all preprocessing, PCA, and clustering. Now I want to merge cluster 1 from object1 and cluster 3 fr ...
scrna-seq single-cell seurat rna-seq R written 3 months ago by biostarukha10
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Comment: C: Survival analysis based on a set of genes for TCGA data
... thank you! I did survival analysis for each gene, but only couple of them are significant. So I thought maybe the combination of more genes will be more significant for survival. ...
written 3 months ago by biostarukha10

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