User: choijamtsm

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choijamtsm50
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Posts by choijamtsm

<prev • 12 results • page 1 of 2 • next >
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R package for GO-BP enrichment analysis with c(symbol, log2foldchange, pvalue)
... Hello everyone. I am trying to get mmu GO-BP pathways from mRNA deseq2 data from mouse: Here is input data: input_genes # Symbol log2FoldChange.case.control. Padj #1 Cnn2 -1.024326 9.830000e-67 #2 Prkg2 -2.7024 ...
R rna-seq go written 5 months ago by choijamtsm50
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Comment: C: EnhancedVolcano: How to coloring custom gene points in volcano plot?
... I followed vignette carefully but still no luck. Is there any alternative solutions to coloring point? ...
written 8 months ago by choijamtsm50
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EnhancedVolcano: How to coloring custom gene points in volcano plot?
... Hello everyone! I am learning to create a volcano plot by using EnhancedVolcano in R. But I am struggling to color custom points (genes). **Here is my input file:** library('EnhancedVolcano') res <- read.table("text.txt", header=TRUE) res$gene <- as.character(res$g ...
enhancedvolcano written 8 months ago by choijamtsm50
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Comment: C: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
... It worked well. thank you so much. ...
written 9 months ago by choijamtsm50
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Comment: C: Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
... Thanks for your response. It works well until this point. x <- Matrix(as.matrix(micedata), sparse = TRUE) but can you tell me the below code: When I execute the below code its shows the following errors. message('--writing 10x output to: file_location ', paste0('mystudy/', gsmid ...
written 9 months ago by choijamtsm50
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Store a scRNA-seq ~gene expression "matrix.txt" as a "matrix.mtx" in R
... Hello everyone! I new here. Actually I downloaded a huge big scRNA-seq .txt file from paper. And I want to analyze this seq data with R ~ "Seurat" package. But in order to do that, I have to convert this .txt format into .mtx file using R Matrix() package!! And scRNA-seq data format looked like t ...
R next-gen rna-seq written 9 months ago by choijamtsm50 • updated 9 months ago by Kevin Blighe69k
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R scatter plot visualization: how to color custom- multiple genes into scatter plot?
... Hello everyone! I tried to make a basic scatter plot with R using gene expression data. #import data: oldmice <- read.table("oldmice.txt", header = TRUE) youngmice <- read.table("youngmice.txt", header = TRUE) Imported data contains: format is the same for both imported ...
R tutorial written 10 months ago by choijamtsm50 • updated 10 months ago by Kevin Blighe69k
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Comment: C: How to label custom multiple gene lists object into volcano plot?
... It works now!! thank you so much ...
written 11 months ago by choijamtsm50
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Comment: C: How to label custom multiple gene lists object into volcano plot?
... Thank you, **1. I altered the cut-offs for p-value and log2 fold change and graph looks nice!** [altered p-value and log2 fold change][1] [1]: https://ibb.co/Z2wNBCt **2. Here are the outputs:** **class(res)** [1] "data.frame" **head(res)** gene log2foldchange pvalue ...
written 11 months ago by choijamtsm50
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Comment: C: How to label custom multiple gene lists object into volcano plot?
... Thank you so much for your reply. I downloaded 'EnhancedVolcano' package then run above command. EnhancedVolcano(res, lab = res$gene, x = 'log2foldchange', y = 'pvalue') **But All of the res$gene labeled on volcano plot**. [Volcano plot Enhanced Volcano res$gene][1] **Actually ...
written 11 months ago by choijamtsm50

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