User: wenbinm

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wenbinm20
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New User
Location:
USA
Last seen:
10 months ago
Joined:
2 years, 1 month ago
Email:
w******@pku.edu.cn

Posts by wenbinm

<prev • 22 results • page 1 of 3 • next >
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Answer: A: Tools for scRNAseq
... I finally discover that I can do this by first inferring CNV (using infercnv for example). Malignant cells have CNV while non-malignant cells don't. Then they can be distinguished. ...
written 10 months ago by wenbinm20
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Comment: C: WGCNA: How to plot gene-trait correlation heatmap
... ComplexHeatmap is a good package. Thanks for sharing.... ...
written 15 months ago by wenbinm20
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Comment: C: WGCNA: How to plot gene-trait correlation heatmap
... The image link: https://ibb.co/jz6hLZW ...
written 15 months ago by wenbinm20
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WGCNA: How to plot gene-trait correlation heatmap
... Hi there, Is there a specific function in WGCNA that can make this kind of plot?![Dendrogram with a heatmap showing Pearson correlation with each gene][1] Or I shall DIY a heatmap myself and put it under the dendrogram. The paper's supplementary info didn't write about this plot in detail. Thanks a ...
wgcna rna-seq R written 15 months ago by wenbinm20 • updated 15 months ago by Buffo1.8k
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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 22 months ago by wenbinm20
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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 22 months ago by wenbinm20 • updated 21 months ago by rogangrant10
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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 2.0 years ago by wenbinm20
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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 2.0 years ago by wenbinm20 • updated 2.0 years 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 2.1 years ago by wenbinm20
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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 2.1 years ago by wenbinm20 • updated 2.1 years ago by Kevin Blighe65k

Latest awards to wenbinm

Popular Question 20 months ago, created a question with more than 1,000 views. For Seurat scRNAseq analysis: what is the mito gene list
Popular Question 20 months ago, created a question with more than 1,000 views. For How to get data from GEO
Popular Question 20 months ago, created a question with more than 1,000 views. For How to map UCSC transcripts to gene symbol?

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