User: Qingyang Xiao

gravatar for Qingyang Xiao
Qingyang Xiao110
Reputation:
110
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Trusted
Location:
Stockholm
Last seen:
2 months, 3 weeks ago
Joined:
9 months, 3 weeks ago
Email:
x************@ki.se

Posts by Qingyang Xiao

<prev • 21 results • page 1 of 3 • next >
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Targeted sequencing and meQTL/eQTM/eQTL
... We are going to do targeted DNA sequencing, targeted methylation sequencing, plus RNA-Seq data. For meQTL/eQTM/eQTL, it seems work well in whole genome sequencing, Can these kinds of analysis be applied into targeted DNA sequencing? Why? And some links or references? Thank you very much! ...
R next-gen snp rna-seq written 12 weeks ago by Qingyang Xiao110
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Forum: Python or R
... Generally speaking, which programming language is better, R and Python? Personally, I used Unix system in supercomputers plus R in my laptop and I didn't find much uncomfortable stuff. For RNA-Seq, from fastq files to differentially expressed gene data and from DE to pathway/co-expression network. ...
next-gen forum alignment rna-seq sequencing written 3 months ago by Qingyang Xiao110 • updated 3 months ago by Kevin Blighe28k
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How to read fastq file with Python
... Hello! What's the meaning of reading fastQ file alone? And how to read fastQ file with Python? ...
next-gen sequencing written 3 months ago by Qingyang Xiao110 • updated 3 months ago by Alex Reynolds25k
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How to have access to TCGA raw data?
... Hello! I have seen tons of paper use TCGA data to verify their own experiment data. But personally I'm struggling that where I can download the TCGA data(fastq file)? It's abstract to me. Could somebody list the website and a short protocol about doing that? Hope you will have a nice weekend! ...
next-gen rna-seq sequencing written 4 months ago by Qingyang Xiao110 • updated 4 months ago by genomax55k
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Answer: A: Identify lncRNAs - search for tools
... If the transcripts are not responsible for coding the proteins, then it's possibly lncRNA. So you can check databases like PFAM, CPC and PhyloCSF. The unmatched parts will provide you some insights of lncRNA. ...
written 6 months ago by Qingyang Xiao110
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identifying contribution of specific cell subpopulation from mixture,with RNA-Seq data
... If the mRNA- Seq data is acuquired from a mixture of cells, such as whole blood cells, can I use some bioinformatics methods to distinguish the contribution of each cell subpopulation? Are there some databases provide with reference cell population expression profile, and corresponding packages? ...
next-gen rna-seq sequencing written 6 months ago by Qingyang Xiao110
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Comment: C: Difference between prediction of protein-protein interaction and mRNA-mRNA inter
... Yes. I only mean co-expression networks, if Im interested in RNA-sEQ. If I understand correctly, you mean STRING can also be used in mRNA network? A bioinoformatician in our group did is to input the pre-defined gene list, based on the module connection(in String for protein interaction), and delet ...
written 6 months ago by Qingyang Xiao110
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Difference between prediction of protein-protein interaction and mRNA-mRNA interaction
... Hello! May I ask what's the different principle between protein-protein interaction and mRNA-mRNA interaction? Can I use some R packages for prediction of protein-protein interaction, for mRNA-mRNA network? e.g.STRINGdb I will be grateful short and clear answer is given, with detail links or public ...
next-gen rna-seq sequencing written 6 months ago by Qingyang Xiao110 • updated 6 months ago by Kevin Blighe28k
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(Closed) How to download sFTP to download files in environment Linux/Unix?
... My data is in the sFTP resource. I'm trying to copy the files to another remote computers and I type the code: sftp tom@123.45.67.89 "tom" is my username And I got the following message: ssh: connect to host 123.45.67.89 port 22: Connection timed out Couldn't read packet: Connection reset b ...
next-gen written 6 months ago by Qingyang Xiao110
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FFPE samples for NGS
... Hello! I have a question of FFPE samples for NGS. Are the fresh/frozen samples superior than FFPE samples for NGS? What I know now is that DNA from FFPE samples are more fragmented than common DNAs. Are there some other characters could distinguish these types of tissue in terms of NGS(here I mean ...
next-gen rna-seq snp sequencing written 7 months ago by Qingyang Xiao110 • updated 7 months ago by Kevin Blighe28k

Latest awards to Qingyang Xiao

Good Question 6 months ago, asked a question that was upvoted at least 5 times. For Difference between tSNE and PCA analysis
Popular Question 6 months ago, created a question with more than 1,000 views. For Difference between tSNE and PCA analysis
Appreciated 8 months ago, created a post with more than 5 votes. For Difference between tSNE and PCA analysis
Student 8 months ago, asked a question with at least 3 up-votes. For Difference between tSNE and PCA analysis

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