User: Mike

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Mike10
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Posts by Mike

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Seurat 2.3.4 installation
... I tried many times to reinstall the previous version of Seurat (2.3.4) using following command ``` install.packages('Seurat', repo = c('satijalab.org/ran/', getOption("repos"))) ``` but after installation, it keeps loading the newest version of Seurat (3.0.0). Could you tell me why and how I can re ...
seurat written 6 months ago by Mike10 • updated 6 months ago by Gordon Smyth39k
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Comment: C: Biomart cannot get multiple genes?
... Thank you so much for the comments, Mike. I think now I understand everything what I did wrong in this work. Thank you very much again! ...
written 12 months ago by Mike10
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Comment: C: Biomart cannot get multiple genes?
... Thanks for the comment, Mike. I am afraid that it is not a case sensitive matching. mca_filter has "Selenop" gene so I tried both values = mca_filter and values = c("Selenop"). But only values = c("Selenop") gives the correct result.  ============================================================== ...
written 12 months ago by Mike10
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Biomart cannot get multiple genes?
... So I am trying get gene information from MCA genes. I used : library(biomaRt) human <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") mca_filter <- mca@var.genes attr <- c("ensembl_gene_id", "hgnc_symbol","chromosome_name",'entrezgene', "start_position", "end_position") Info < ...
biomart R written 12 months ago by Mike10
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biomaRt question (missing gene information?)
... I am usingPeripheral Blood Mononuclear Cells (PBMC) data from Seurat website (https://satijalab.org/seurat/pbmc3k_tutorial.html) I am trying to get gene information by using biomaRt package on R.   library(biomaRt) ensembl <- useMart("ensembl",                     dataset = "hsapiens_gene_ensem ...
biomart R written 13 months ago by Mike10 • updated 13 months ago by Mike Smith4.0k

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