User: wenbinm

gravatar for wenbinm
wenbinm0
Reputation:
0
Status:
New User
Last seen:
1 month, 2 weeks ago
Joined:
1 year ago
Email:
w******@pku.edu.cn

Profile information, website and location are not shown for new users.

This helps us discourage the inappropriate use of our site.

Posts by wenbinm

<prev • 21 results • page 1 of 3 • next >
0
votes
1
answer
169
views
1
answers
Comment: C: WGCNA: How to plot gene-trait correlation heatmap
... ComplexHeatmap is a good package. Thanks for sharing.... ...
written 7 weeks ago by wenbinm0
0
votes
1
answer
169
views
1
answers
Comment: C: WGCNA: How to plot gene-trait correlation heatmap
... The image link: https://ibb.co/jz6hLZW ...
written 7 weeks ago by wenbinm0
0
votes
1
answer
169
views
1
answer
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 7 weeks ago by wenbinm0 • updated 7 weeks ago by Buffo1.6k
0
votes
2
answers
1.4k
views
2
answers
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 9 months ago by wenbinm0
2
votes
2
answers
1.4k
views
2
answers
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 9 months ago by wenbinm0 • updated 8 months ago by rogangrant0
0
votes
1
answer
525
views
1
answers
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 11 months ago by wenbinm0
2
votes
1
answer
525
views
1
answer
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 11 months ago by wenbinm0 • updated 11 months ago by mary20
0
votes
1
answer
1.4k
views
1
answers
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 11 months ago by wenbinm0
2
votes
1
answer
1.4k
views
1
answer
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 11 months ago by wenbinm0 • updated 11 months ago by Kevin Blighe46k
0
votes
2
answers
1.1k
views
2
answers
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 11 months ago by wenbinm0

Latest awards to wenbinm

Popular Question 7 months ago, created a question with more than 1,000 views. For Seurat scRNAseq analysis: what is the mito gene list
Popular Question 7 months ago, created a question with more than 1,000 views. For How to get data from GEO
Popular Question 7 months ago, created a question with more than 1,000 views. For How to map UCSC transcripts to gene symbol?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1527 users visited in the last hour