User: Xingyu Yang

gravatar for Xingyu Yang
Xingyu Yang260
Reputation:
260
Status:
Trusted
Location:
Atlanta
Website:
http://bioyang.com/
Scholar ID:
Google Scholar Page
Last seen:
3 years, 6 months ago
Joined:
5 years, 9 months ago
Email:
x******@gmail.com

about me

Posts by Xingyu Yang

<prev • 39 results • page 1 of 4 • next >
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Answer: A: Installation Of Tophat -1.1.4
... I understand this is a very old post. However, after following the top rated answer, I still get the same error. Fix it by rename the `XXX/include/bam/version.h` to `version.hpp`. The source code (`bam.h`) includes `version.hpp` rather than `version.h` ...
written 4.1 years ago by Xingyu Yang260 • updated 10 weeks ago by RamRS24k
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DAVID or GSEA for functional analysis of RNAseq
... I want to do functional analysis of RNAseq data. I noticed that two most famous approach "DAVID" and "GSEA" use very different way to do this. Thus, the pathways I obtained from them show little overlap.   Just want to ask, which one generally works better? Or both of them have their reason, it's ...
david rna-seq gsea functional analysis written 4.1 years ago by Xingyu Yang260
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Do bioinformatics PhD students need Statistics dual degree?
... Hi all, I'm currently a PhD student majoring in bioinformatics. I want to find a job after graduation.  Worth to have a statistics dual degree? To obtain the degree, I need to take additional 10 courses. Taking the additional courses might take time and decrease the time spend on research. Therefo ...
dual degree bioinformatics phd job statistics written 5.2 years ago by Xingyu Yang260 • updated 5.2 years ago by Charles Warden7.4k
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Comment: C: PhD in Bioinformatics: to continue, or not to continue? That is the question--
... I would suggest you change a lab. 7 years is too long to get a bioinformatics degree. I know many students graduate in 3 years with couple very good publication.  ...
written 5.5 years ago by Xingyu Yang260
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Comment: C: why expression value must be log2 transformed before further analysis, such diff
... Who told you this? Log transformed expression are easier to detect DEG with low expression level. However, I never heard it's a must to log transformed them.  ...
written 5.5 years ago by Xingyu Yang260
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Comment: C: Profile-based Genome Alignment
... I don't know any existing software can do that. If you find one, could you please post it here? Or if you can develop one, I believe it can be very promising (Can be a replacement of multiple alignemnt).  ...
written 5.6 years ago by Xingyu Yang260
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Comment: C: What is the difference between refrence genome and annotation ?
... ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens/GFF/ref_GRCh38_top_level.gff3.gz ...
written 5.6 years ago by Xingyu Yang260
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Comment: C: Profile-based Genome Alignment
... Yes, I think you are talking about multiple alignment. I don't think there exist any tools can do multiple alignment to 200 genomes(you may try and welcome to prove me wrong) for computation cost reason.  ...
written 5.6 years ago by Xingyu Yang260
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Comment: C: Profile-based Genome Alignment
... What's your reference? Or you use multiple alignment? I don't think you can use multiple alignement to align 200 genomes, so you must have a reference. You can just align the  new genome to the reference. ...
written 5.6 years ago by Xingyu Yang260
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Comment: C: What is the difference between refrence genome and annotation ?
... It include everything. Like different format of annotation, annotation of ncRNA, reference sequence, indexed reference sequences.  If you just want the annotation file, find it on ncbi ftp:ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens. Annotation file are in the GFF folder. The annotation file includ ...
written 5.6 years ago by Xingyu Yang260

Latest awards to Xingyu Yang

Popular Question 3.6 years ago, created a question with more than 1,000 views. For How To Run Tmhmm In Interproscan 5 Standalone Version
Appreciated 4.1 years ago, created a post with more than 5 votes. For A: Will Python Take The Place Of R?
Popular Question 4.8 years ago, created a question with more than 1,000 views. For How To Run Tmhmm In Interproscan 5 Standalone Version
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Masters In Bioinformatics Vs Masters In Information Technology (Computer Science
Supporter 5.2 years ago, voted at least 25 times.
Teacher 5.6 years ago, created an answer with at least 3 up-votes. For A: Masters In Bioinformatics Vs Masters In Information Technology (Computer Science

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