User: Xiaokang ZH

gravatar for Xiaokang ZH
Xiaokang ZH40
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40
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14 hours ago
Joined:
2 years, 10 months ago
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z*********@gmail.com

Posts by Xiaokang ZH

<prev • 25 results • page 1 of 3 • next >
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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 days ago by Xiaokang ZH40 • updated 10 days ago by ATpoint21k
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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 15 months ago by Xiaokang ZH40 • updated 15 months ago by xanderpico170
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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 17 months 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 17 months 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 17 months 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 17 months ago by Xiaokang ZH40 • updated 16 months ago by xanderpico170
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Comment: C: Align protein sequence to Pfam file using HMMER3.0 (hmmalign)
... Thank you very much! ...
written 18 months ago by Xiaokang ZH40
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Comment: C: Align protein sequence to Pfam file using HMMER3.0 (hmmalign)
... Thank you. But why hmmscan, instead of hmmsearch? Since I found an article comparing them [here][1]. It seems that they have the same output, but hmmsearch is faster? [1]: https://cryptogenomicon.org/2011/05/27/hmmscan-vs-hmmsearch-speed-the-numerology/ ...
written 18 months ago by Xiaokang ZH40
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Align protein sequence to Pfam file using HMMER3.0 (hmmalign)
... I'm using HMMER 3.0 (hmmalign to be specific) to align the whole proteome of Human to Pfam file. I got the proteome from https://www.ensembl.org/info/data/ftp/index.html, got the Pfam file from: ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam31.0/, and downloaded the file Pfam-A.hmm.gz With ...
hmmer protein pfam written 18 months ago by Xiaokang ZH40 • updated 16 months ago by Biostar ♦♦ 20
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Comment: C: How to perform DESeq2 based on paired sample test?
... I've deleted those two samples completely, including the levels 1 and 7 in fishGroup: > levels(colData$fishGroup) [1] "2" "3" "4" "5" "6" "8" ...
written 2.2 years ago by Xiaokang ZH40

Latest awards to Xiaokang ZH

Popular Question 8 months ago, created a question with more than 1,000 views. For How many index files will be generated from hisat2-build
Popular Question 11 months ago, created a question with more than 1,000 views. For How many index files will be generated from hisat2-build
Popular Question 13 months ago, created a question with more than 1,000 views. For How to perform DESeq2 based on paired sample test?
Popular Question 13 months ago, created a question with more than 1,000 views. For Differentially Expressed Genes Analysis with RNA-Seq data
Popular Question 16 months ago, created a question with more than 1,000 views. For Effective length in normalisation for reads counts

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