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User: Chen

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Chen • 920
Reputation:
920
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Last seen:
3 months, 2 weeks ago
Joined:
7 years, 3 months ago
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b********@gmail.com

Computer Science Ph.D. 

Fan of Istvan Albert 

Research Area: Bioinformatics, Algorithms, Machine Learning

Posts by Chen

<prev • 100 results • page 1 of 10 • next >
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Comment: C: How can I contribute to the Bioinformatics community as a Software Engineer
... By contributing, I mean writing software or applications ...
written 12 months ago by Chen • 920
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Forum: How can I contribute to the Bioinformatics community as a Software Engineer
... I got my Ph.D. in Computer Science with research directions of bioinformatics and computational biology. I published several first-author papers in journal Bioinformatics and conferences like RECOMB. I also have a Master degree in Genomics. Now I am a full-time Software Engineer in Silicon Valley, ...
bioinformatics forum written 12 months ago by Chen • 920 • updated 12 months ago by genebow • 150
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Comment: C: How to validate the SNP calling pipeline?
... Here is 300x coverage NGS reads for human in FASTQ file format: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/ ...
written 12 months ago by Chen • 920
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What is the difference between Bioconda and Galaxy?
... Previously people suggest me to put my tool into Galaxy, now people suggest me to put my tool into Bioconda. After spending more than one day to put my recent tool into Bioconda, I am wondering does anyone know their differences? Which one is better to make your tool more accessible? Thanks! ...
bioconda galaxy bioinformatics tools written 15 months ago by Chen • 920 • updated 15 months ago by Friederike ♦ 5.2k
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Comment: C: Can SNP array handle clustered SNPs
... I agree, and thank you for the information. I will double think before I ask next time. Please delete if possible. ...
written 19 months ago by Chen • 920
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Can SNP array handle clustered SNPs
... Can SNP arrays such as Affymetrix genome-wide SNP array 6.0 handle clustered SNPs. By clustered SNPs I mean SNPs that are very close to each other, for instance, SNPs that are closer than 10 bp? ...
snp calling snp array snp written 19 months ago by Chen • 920
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Comment: C: RNA-Seq Variant Calling
... Can you share the command lines you used? ...
written 19 months ago by Chen • 920
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Comment: C: Is there a easy to use GATK pipeline for SNP calling?
... Hi swimmer, thank you very much for the suggestions. Do you think https://gencore.bio.nyu.edu/variant-calling-pipeline/ is a good command pipeline that I can follow? This is the kind of pipeline I am looking for, but I am not sure if they miss something important. ...
written 19 months ago by Chen • 920
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Is there a easy to use GATK pipeline for SNP calling?
... With full respect, GATK is a good tool for SNP calling. But the tutorial on GATK website is too complex, I get lost in the details. Is there an easy to use a list of GATK commands for SNP calling? That I can copy and paste, with changing of just input file names, and maybe few parameters? ...
gatk written 19 months ago by Chen • 920 • updated 7 months ago by johannes.koester • 10
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Comment: C: Where Can I Find A Good Database Of The Repeat Regions Of The Human Genome ?
... is the database 0-based or 1 based? ...
written 20 months ago by Chen • 920

Latest awards to Chen

Great Question 6 months ago, created a question with more than 5,000 views. For Any difference between capital letter(ATGC) and lowercase letter(atgc) in hg19 fasta file
Student 9 months ago, asked a question with at least 3 up-votes. For Which Bioinformatics Tools Are Written In Python
Student 9 months ago, asked a question with at least 3 up-votes. For Any difference between capital letter(ATGC) and lowercase letter(atgc) in hg19 fasta file
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to validate the SNP calling pipeline?
Popular Question 9 months ago, created a question with more than 1,000 views. For Question about genotype phased PQ and PS in VCF file format 4.1
Popular Question 9 months ago, created a question with more than 1,000 views. For C++ how to read VCF file in indexed bgzip format?
Popular Question 12 months ago, created a question with more than 1,000 views. For C++ how to read VCF file in indexed bgzip format?
Good Question 12 months ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Popular Question 12 months ago, created a question with more than 1,000 views. For C++ tools are hard to install for biologist, why the community stick on it?
Popular Question 12 months ago, created a question with more than 1,000 views. For How to find the self aligned repeat region in human genome
Good Question 13 months ago, asked a question that was upvoted at least 5 times. For Which Bioinformatics Tools Are Written In Python
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: How to validate the SNP calling pipeline?
Popular Question 13 months ago, created a question with more than 1,000 views. For C++ how to read VCF file in indexed bgzip format?
Popular Question 14 months ago, created a question with more than 1,000 views. For C++ how to read VCF file in indexed bgzip format?
Appreciated 15 months ago, created a post with more than 5 votes. For Which Bioinformatics Tools Are Written In Python
Popular Question 16 months ago, created a question with more than 1,000 views. For C++ how to read VCF file in indexed bgzip format?
Popular Question 17 months ago, created a question with more than 1,000 views. For C++ how to read VCF file in indexed bgzip format?
Popular Question 18 months ago, created a question with more than 1,000 views. For C++ how to read VCF file in indexed bgzip format?
Great Question 19 months ago, created a question with more than 5,000 views. For Which Bioinformatics Tools Are Written In Python
Voter 19 months ago, voted more than 100 times.
Centurion 19 months ago, created 100 posts.
Popular Question 20 months ago, created a question with more than 1,000 views. For C++ how to read VCF file in indexed bgzip format?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: How to validate the SNP calling pipeline?
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How to find the self aligned repeat region in human genome
Popular Question 2.0 years ago, created a question with more than 1,000 views. For C++ how to read VCF file in indexed bgzip format?
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