User: Leandro Lima

gravatar for Leandro Lima
Leandro Lima880
Reputation:
880
Status:
Trusted
Location:
San Francisco, CA
Website:
http://www.ime.usp.br/...
Twitter:
lelimat
Scholar ID:
Google Scholar Page
Last seen:
15 hours ago
Joined:
5 years, 7 months ago
Email:
l********@gmail.com

Bioinformatics Software Engineer at Gladstone Institutes

Posts by Leandro Lima

<prev • 88 results • page 1 of 9 • next >
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Answer: A: visualize CNV data based on WGS
... Hi, Bogdan. Have you tried [IGV][1]? You can load the BAMs and the BED files to check. Leandro [1]: http://software.broadinstitute.org/software/igv/ ...
written 15 hours ago by Leandro Lima880
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Comment: C: Machine Learning/Deep Learning approaches to integrate genotype and annotation i
... Thanks for the link, Hussain. They use genotype information, but they are not using any annotation (e.g. functional impact, frequency, etc.). ...
written 2 days ago by Leandro Lima880
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Machine Learning/Deep Learning approaches to integrate genotype and annotation information for predictions?
... Hi, everyone. I'm looking for some material (papers/tools) showing approaches to integrate genotype information (e.g. from WGS) and the variant/gene annotations to do predictions (e.g. age of onset, phenotype) with ML/DL. Any recommendations? Thanks in advance, Leandro ...
annotation deep learning machine learning written 4 days ago by Leandro Lima880 • updated 4 days ago by Hussain Ather680
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Comment: C: ./ Vs "0/0" In Vcf Files
... This happens when there is more than one alternative allele. Suppose your reference is A and the most common alt. allele is C, but G and T can also occur. Then, AC -> 0/1 AG -> 0/2 AT -> 0/3 I believe this is common in indels. ...
written 7 weeks ago by Leandro Lima880
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Answer: A: Data retrieval from GEO
... I believe GEOmetadb could help you: https://gbnci-abcc.ncifcrf.gov/geo/gsm.php R package: http://bioconductor.org/packages/2.2/bioc/html/GEOmetadb.html ...
written 4 months ago by Leandro Lima880
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Comment: C: CNV frequencies and MAF
... Hi @smarini1. Sorry, but for now it's only possible to check for occurrence in a certain number of samples (and DGV gives this information), not the frequency. Leandro ...
written 11 months ago by Leandro Lima880
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Comment: C: Semantic Similarity against all MeSH categories
... What's the size of your file? Did you try to download again? ...
written 11 months ago by Leandro Lima880
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Comment: C: Semantic Similarity against all MeSH categories
... This error is actually coming from RSQLite. I got a similar problem, when using GEOmetadb. ` Error in rsqlite_send_query(conn@ptr, statement) : basic_string::_M_replace_aux ` The problem was that for some reason the sqlite file was with size=0. I downloaded the file again, created the connection ...
written 13 months ago by Leandro Lima880
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Comment: C: Gatk - Haplotypecaller Is So Slow, What Is Faster And As Good?
... You can find more info here: https://software.broadinstitute.org/gatk/documentation/article?id=6201 ...
written 14 months ago by Leandro Lima880
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Comment: C: help geometadb r package
... Hi Andreia. Did you solve this problem? ...
written 15 months ago by Leandro Lima880

Latest awards to Leandro Lima

Popular Question 10 weeks ago, created a question with more than 1,000 views. For CNV frequencies and MAF
Popular Question 11 months ago, created a question with more than 1,000 views. For CNV frequencies and MAF
Popular Question 16 months ago, created a question with more than 1,000 views. For CNV frequencies and MAF
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: Difference Between "Mate Pair" And "Pair-End"
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: 1000 Genomes Ld Calculation
Appreciated 3.4 years ago, created a post with more than 5 votes. For A: 1000 Genomes Ld Calculation
Good Answer 3.4 years ago, created an answer that was upvoted at least 5 times. For A: 1000 Genomes Ld Calculation
Autobiographer 3.8 years ago, has more than 80 characters in the information field of the user's profile.
Voter 3.8 years ago, voted more than 100 times.
Supporter 3.8 years ago, voted at least 25 times.
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: What Is The Recommended Way To Use Bwa On Files Containing Haplotypes Of An Exom
Teacher 4.7 years ago, created an answer with at least 3 up-votes. For A: What'S The Meaning Of "Random Walk" In The Gsea Paper Published By The Broad Ins
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: Need Recommendation On Good Tutorials For Performing Gwas
Teacher 4.9 years ago, created an answer with at least 3 up-votes. For A: How To Visualize Custom 2D Genomic Data In A Genome Browser?
Teacher 5.0 years ago, created an answer with at least 3 up-votes. For A: Should I Start With Python 3?
Teacher 5.5 years ago, created an answer with at least 3 up-votes. For A: Gene Coexpression Networks

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