User: wenbinm

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wenbinm0
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Posts by wenbinm

<prev • 18 results • page 1 of 2 • next >
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Comment: C: Seurat scRNAseq analysis: what is the mito gene list
... It works. Thank you! It seems that Seurat is always using these 13 genes: 'Nd1','Nd2','Co1','Co2','Atp8','Atp6','Co3','Nd3','Nd4l','Nd4','Nd5','Nd6','Cytb' ...
written 5 months ago by wenbinm0
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Seurat scRNAseq analysis: what is the mito gene list
... Hi there, I am trying to analyze 10X genomics output with Seurat. After reading in data using "Read10X" function and create an Seurat object, I am stuck at this step: > mito.genes <- grep(pattern = "^MT-", x = rownames(x = my_data@data), value = TRUE) For the data I have, row names of the ...
rna-seq scrnaseq written 5 months ago by wenbinm0 • updated 4 months ago by rogangrant0
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Comment: C: Are TCGA data from UCSC cancer browser and TCGAbiolinks different?
... Thank you for your quick response! I downloaded UCSC Xena data from here, unzipped it and opened the file with excel: https://tcga.xenahubs.net/download/TCGA.BRCA.sampleMap/HiSeqV2.gz Then I took a look at SOX10 expression data and the first 5 numbers are 6.5221 0 8.308 6.3628 0.5819. Maybe I make ...
written 7 months ago by wenbinm0
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Are TCGA data from UCSC cancer browser and TCGAbiolinks different?
... Hi there, I downloaded TCGA BRCA RNAseq data from UCSC cancer browser or used TCGAbiolinks: library(TCGAbiolinks) query <- GDCquery(project = 'TCGA-BRCA', data.category = 'Transcriptome Profiling', data.type = 'Gene Expression Quantification', workflow.type = 'HTSeq - Counts') GDCdo ...
tcga rna-seq written 7 months ago by wenbinm0 • updated 7 months ago by mary20
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Comment: C: How to get data from GEO
... Thank you for your response! I am sorry I made a mistake here. library(GEOquery) will download 'series matrix' data. I met the problem when I try to directly read in downloaded series matrix data: data <- getGEO(filename = 'GSE2034_series_matrix.txt.gz' ) data <- as.data.frame(exprs( ...
written 7 months ago by wenbinm0
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How to get data from GEO
... Hi there, I am using R package GEOquery to download data from GEO. I use library(GEOquery) library(Biobase) data <- getGEO('GSE2034') data <- as.data.frame(exprs(data[[1]])) #extracting expression data Then I have a file named "GSE2034_family.soft.gz" downloaded. So far thi ...
microarray written 7 months ago by wenbinm0 • updated 7 months ago by Kevin Blighe41k
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Comment: C: How to map UCSC transcripts to gene symbol?
... I ended up finding a refseq annotation file called "refMrna.fa.gz" on UCSC website which gives me mapping between transcript to names. After all, thank you for your reply! ...
written 7 months ago by wenbinm0
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Comment: C: How to map UCSC transcripts to gene symbol?
... I ended up finding a refseq annotation file called "refMrna.fa.gz" on UCSC website which gives me mapping between transcript to names. After all, thank you for your reply! ...
written 7 months ago by wenbinm0
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How to map UCSC transcripts to gene symbol?
... Hi there, I would like to map UCSC transcripts id (mouse genome mm10, I downloaded the transcripts id from [http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/refMrna.fa.gz][1]) to gene symbol. I have a list of transcript id like 'NR_046233 2' and want to get a list of corresponding gene symbol ...
genome assembly rna-seq written 8 months ago by wenbinm0 • updated 8 months ago by Alex Reynolds28k
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How to do survival analysis?
... Hi there, I would like to find genes correlated with poor prognosis. I am doing a simple survival analysis: 1. divide patients into two groups by gene expression (using median as cutoff). 2. find genes significantly correlated with overall survival time (using coxph function in R). 3. check whe ...
prognosis survival analysis cancer written 8 months ago by wenbinm0 • updated 6 weeks ago by Kevin Blighe41k

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