User: Xiaokang ZH

gravatar for Xiaokang ZH
Xiaokang ZH40
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4 months ago
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3 years, 8 months ago
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z*********@gmail.com

Posts by Xiaokang ZH

<prev • 29 results • page 1 of 3 • next >
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How to show an attribute next to the label in Cytoscape
... The label shown on the node in Cytoscape is the name of that node. Can I also show an attribute next to the label? The context is: in my network, each node is a gene. When I originally import the network, the used name is the gene symbol which will be shown on the network as the label of that node. ...
cytoscape written 7 months ago by Xiaokang ZH40 • updated 7 months ago by Wietje210
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Comment: C: How they get such a low adjusted P value in differential analysis of proteomics
... Thank you Leite. The data I have is already processed abundance. I'll check out Perseus. ...
written 8 months ago by Xiaokang ZH40
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Comment: C: How they get such a low adjusted P value in differential analysis of proteomics
... Thank you! That's a good point. I did find 3 outliers with PCA and after removing them, the `p-adj` became more normal (I use to have one comparison of two groups with all `p-adj = 1` and now they look normal. But still, they are still very high. A quick glance at the lowest ones: 0.00827, 0.0611, 0 ...
written 8 months ago by Xiaokang ZH40
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How they get such a low adjusted P value in differential analysis of proteomics data?
... I'm new to proteomics data and my experience with it is quite different from transcriptomics data (RNA-Seq). I got some protein abundance data of samples from control group and exposure group (in vivo experiment exposing fish to toxicant, 10 samples in each group). The purpose is to find out the dif ...
proteomics differential analysis p value fdr dep written 8 months ago by Xiaokang ZH40
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How to compare the alignment to genome and transcriptome
... I'm analysing RNA-Seq data of cod (Gadus morhua) which is a non-model species, meaning that the quality of its genome and annotation is not as good as model species such as human and mouse. The downstream analysis of the RNA-Seq alignment is to do differential expression analysis and pathway enrichm ...
genome alignment rna-seq transcriptome written 10 months ago by Xiaokang ZH40 • updated 10 months ago by ATpoint36k
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Cytoscape: select edges that are the interactions between two networks
... I have two networks: A and B. B is a subset of A. I'm now working on A, and I'd like to select all the edges appearing in B, so that I can color those edges in A to highlight them. How to do this in Cytoscape? ...
interaction network cytoscape written 2.1 years ago by Xiaokang ZH40 • updated 2.1 years ago by xanderpico210
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Comment: C: Filter out the information from other organisms in STRING
... Thank you! From the webpage you provide, there's a file "*protein.links.full*", where it provides scores from different channels, and there will be two columns for each channel. For an example, "database" and "database_transferred" for the specific species itself and information from other species ( ...
written 2.3 years ago by Xiaokang ZH40
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Comment: C: Filter out the information from other organisms in STRING
... Hi Pierre, thank you for reminding. The other post is now deleted. ...
written 2.3 years ago by Xiaokang ZH40
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Filter out the information from other organisms in STRING
... I'm using STRING to get the interaction between some interesting genes in cod (Gadus morhua). On the page of "search", you can choose the organism you're interested in, and STRING will only give you the genes that they have a record in their database for cod, which is what I want. And then you'll ge ...
ppi string written 2.3 years ago by Xiaokang ZH40
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Multiple networks integrated into one figure in Cytoscape
... I have a list of genes (let’s call it L), and I want to see how they work differently in 3 different species (human, zebrafish and cod). Of course, the 3 species don’t have all the genes in the list, besides, the interactions between genes are different across 3 species. Firstly, I search the genes ...
network cytoscape written 2.3 years ago by Xiaokang ZH40 • updated 2.2 years ago by xanderpico210

Latest awards to Xiaokang ZH

Popular Question 4 months ago, created a question with more than 1,000 views. For Cytoscape: select edges that are the interactions between two networks
Popular Question 8 months ago, created a question with more than 1,000 views. For Cytoscape: select edges that are the interactions between two networks
Popular Question 9 months ago, created a question with more than 1,000 views. For Must I sort the .bam or .sam file before do the feature count?
Popular Question 9 months ago, created a question with more than 1,000 views. For Must I sort the .bam or .sam file before do the feature count?
Popular Question 18 months ago, created a question with more than 1,000 views. For How many index files will be generated from hisat2-build
Popular Question 21 months ago, created a question with more than 1,000 views. For How many index files will be generated from hisat2-build
Popular Question 24 months ago, created a question with more than 1,000 views. For How to perform DESeq2 based on paired sample test?
Popular Question 24 months ago, created a question with more than 1,000 views. For Differentially Expressed Genes Analysis with RNA-Seq data
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Effective length in normalisation for reads counts

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