User: Leandro Lima

gravatar for Leandro Lima
Leandro Lima900
Reputation:
900
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Location:
San Francisco, CA
Website:
http://www.ime.usp.br/...
Twitter:
lelimat
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Google Scholar Page
Last seen:
4 days, 21 hours ago
Joined:
6 years, 3 months ago
Email:
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Bioinformatics Software Engineer at Gladstone Institutes

Posts by Leandro Lima

<prev • 92 results • page 1 of 10 • next >
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Answer: A: Genome Version Of Targetscan
... hg19. More info: http://www.targetscan.org/cgi-bin/targetscan/data_download.vert72.cgi ...
written 14 days ago by Leandro Lima900
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Comment: C: List Of Genome Sequencing Centers/Institutes
... It looks like only the Google Maps link is working now. ...
written 4 months ago by Leandro Lima900
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Comment: C: How to use GRCh38 as reference for Annotating the variants using Annovar?
... This also might be helpful: https://www.biostars.org/p/196985/ ...
written 4 months ago by Leandro Lima900
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Answer: A: SnpMatrix from VCF file
... This should also work (I'm assuming that everything that is not 0/0, 0/1 or 1/1 should be considered as 0): vcf=genotypes.vcf vcftools --vcf $vcf --extract-FORMAT-info GT --out requiredFormat # Creating SNP.txt awk '{$1=$1":"$2; $2=""; print $0}' requiredFormat.GT.FOR ...
written 6 months ago by Leandro Lima900
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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 8 months ago by Leandro Lima900
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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 8 months ago by Leandro Lima900
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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 8 months ago by Leandro Lima900 • updated 8 months ago by Hussain Ather880
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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 9 months ago by Leandro Lima900
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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 12 months ago by Leandro Lima900
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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 19 months ago by Leandro Lima900

Latest awards to Leandro Lima

Student 25 days ago, asked a question with at least 3 up-votes. For CNV frequencies and MAF
Popular Question 6 weeks ago, created a question with more than 1,000 views. For CNV frequencies and MAF
Popular Question 10 months ago, created a question with more than 1,000 views. For CNV frequencies and MAF
Popular Question 20 months ago, created a question with more than 1,000 views. For CNV frequencies and MAF
Popular Question 2.1 years ago, created a question with more than 1,000 views. For CNV frequencies and MAF
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Difference Between "Mate Pair" And "Pair-End"
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: 1000 Genomes Ld Calculation
Appreciated 4.1 years ago, created a post with more than 5 votes. For A: 1000 Genomes Ld Calculation
Good Answer 4.1 years ago, created an answer that was upvoted at least 5 times. For A: 1000 Genomes Ld Calculation
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Voter 4.4 years ago, voted more than 100 times.
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Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: 1000 Genomes Ld Calculation
Teacher 5.4 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 5.4 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 5.5 years ago, created an answer with at least 3 up-votes. For A: Need Recommendation On Good Tutorials For Performing Gwas
Teacher 5.6 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 5.7 years ago, created an answer with at least 3 up-votes. For A: Should I Start With Python 3?
Teacher 6.1 years ago, created an answer with at least 3 up-votes. For A: Gene Coexpression Networks

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